X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 293.0
Details 5% PEG 3350, 0.2 M MgCl2, 20% 1,2-propanediol, pH Hepes 7.5, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 232.19 α = 90
b = 232.19 β = 90
c = 168.31 γ = 90
Symmetry
Space Group P 43 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 104
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR345 mirrors 2010-03-29
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5417 -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
3.32 17 97.0 0.175 -- -- 4.4 -- 65555 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
3.32 3.44 93.7 0.961 -- -- 3.5 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
-- 3.32 17.0 -- 0.0 -- 65342 6560 96.6 -- -- 0.282 0.3315 --
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 3.32 3.34 -- 117 1002 0.3966 0.4187 -- --
X Ray Diffraction 3.34 3.37 -- 136 1132 0.3798 0.3982 -- --
X Ray Diffraction 3.37 3.39 -- 144 1080 0.3765 0.376 -- --
X Ray Diffraction 3.39 3.41 -- 115 1153 0.3904 0.4509 -- --
X Ray Diffraction 3.41 3.44 -- 118 1116 0.3993 0.4189 -- --
X Ray Diffraction 3.44 3.46 -- 127 1118 0.3904 0.3932 -- --
X Ray Diffraction 3.46 3.49 -- 134 1112 0.3773 0.4329 -- --
X Ray Diffraction 3.49 3.52 -- 110 1140 0.3881 0.368 -- --
X Ray Diffraction 3.52 3.55 -- 115 1140 0.3836 0.4252 -- --
X Ray Diffraction 3.55 3.57 -- 133 1109 0.3744 0.3693 -- --
X Ray Diffraction 3.57 3.6 -- 126 1132 0.3639 0.4239 -- --
X Ray Diffraction 3.6 3.64 -- 123 1152 0.3803 0.4181 -- --
X Ray Diffraction 3.64 3.67 -- 144 1138 0.3636 0.4267 -- --
X Ray Diffraction 3.67 3.7 -- 117 1131 0.3694 0.3893 -- --
X Ray Diffraction 3.7 3.74 -- 151 1156 0.3665 0.4294 -- --
X Ray Diffraction 3.74 3.77 -- 131 1151 0.3519 0.3656 -- --
X Ray Diffraction 3.77 3.81 -- 127 1150 0.3529 0.408 -- --
X Ray Diffraction 3.81 3.85 -- 132 1156 0.3374 0.3646 -- --
X Ray Diffraction 3.85 3.89 -- 118 1174 0.3146 0.3705 -- --
X Ray Diffraction 3.89 3.93 -- 118 1188 0.3364 0.3868 -- --
X Ray Diffraction 3.93 3.97 -- 122 1162 0.3055 0.33 -- --
X Ray Diffraction 3.97 4.02 -- 144 1170 0.3105 0.3936 -- --
X Ray Diffraction 4.02 4.07 -- 137 1163 0.3029 0.3533 -- --
X Ray Diffraction 4.07 4.12 -- 130 1180 0.3007 0.3764 -- --
X Ray Diffraction 4.12 4.17 -- 135 1165 0.296 0.3336 -- --
X Ray Diffraction 4.17 4.23 -- 132 1202 0.2777 0.3359 -- --
X Ray Diffraction 4.23 4.29 -- 134 1180 0.2784 0.3158 -- --
X Ray Diffraction 4.29 4.35 -- 138 1182 0.2604 0.3223 -- --
X Ray Diffraction 4.35 4.42 -- 144 1173 0.277 0.3448 -- --
X Ray Diffraction 4.42 4.49 -- 127 1208 0.2482 0.3135 -- --
X Ray Diffraction 4.49 4.57 -- 116 1220 0.2756 0.3237 -- --
X Ray Diffraction 4.57 4.65 -- 115 1227 0.2697 0.3384 -- --
X Ray Diffraction 4.65 4.73 -- 137 1181 0.2437 0.2853 -- --
X Ray Diffraction 4.73 4.83 -- 126 1224 0.2419 0.2911 -- --
X Ray Diffraction 4.83 4.93 -- 122 1216 0.2583 0.3241 -- --
X Ray Diffraction 4.93 5.04 -- 146 1196 0.2518 0.3055 -- --
X Ray Diffraction 5.04 5.17 -- 132 1187 0.2357 0.2975 -- --
X Ray Diffraction 5.17 5.3 -- 127 1220 0.2427 0.3067 -- --
X Ray Diffraction 5.3 5.45 -- 138 1198 0.267 0.3347 -- --
X Ray Diffraction 5.45 5.62 -- 120 1243 0.2712 0.3346 -- --
X Ray Diffraction 5.62 5.82 -- 130 1201 0.2847 0.3907 -- --
X Ray Diffraction 5.82 6.04 -- 136 1219 0.2791 0.2972 -- --
X Ray Diffraction 6.04 6.3 -- 138 1212 0.2829 0.3898 -- --
X Ray Diffraction 6.3 6.61 -- 133 1214 0.2548 0.3112 -- --
X Ray Diffraction 6.61 7.0 -- 161 1203 0.2242 0.2676 -- --
X Ray Diffraction 7.0 7.5 -- 143 1215 0.2125 0.2872 -- --
X Ray Diffraction 7.5 8.17 -- 150 1221 0.2038 0.2538 -- --
X Ray Diffraction 8.17 9.19 -- 139 1235 0.1906 0.2545 -- --
X Ray Diffraction 9.19 11.03 -- 136 1257 0.1922 0.2445 -- --
X Ray Diffraction 11.03 17.0 -- 136 1278 0.2429 0.2606 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 105.535
Anisotropic B[1][1] 14.622
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 14.622
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -29.243
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.0079
c_angle_d 1.2839
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.67
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 16618
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 0

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing version: 2.1.4
CNS refinement
PDB_EXTRACT data extraction version: 3.10