X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.15
Details 6 % PEG 4000, 5 mM magnesium acetate and 50 mM ADA (pH 6.5)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.28 α = 90
b = 146.28 β = 90
c = 46.94 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 -- 2016-04-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID

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
1.9 146.28 99.8 0.088 0.088 6.7 7.0 -- 31032 -- -- 21.9
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)
1.9 2.0 99.6 0.47 0.47 1.6 6.9 --

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
MOLECULAR REPLACEMENT 1.9 44.696 -- 1.35 -- 30765 1535 99.73 -- 0.206 0.2043 0.2374 --
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 1.9001 1.9614 -- 116 2621 0.2457 0.3343 0.0 100.0
X Ray Diffraction 1.9614 2.0315 -- 132 2597 0.2144 0.2522 0.0 100.0
X Ray Diffraction 2.0315 2.1128 -- 117 2622 0.2123 0.241 0.0 100.0
X Ray Diffraction 2.1128 2.209 -- 131 2641 0.2106 0.2241 0.0 100.0
X Ray Diffraction 2.209 2.3254 -- 140 2623 0.2123 0.2436 0.0 100.0
X Ray Diffraction 2.3254 2.4711 -- 150 2621 0.2069 0.2484 0.0 100.0
X Ray Diffraction 2.4711 2.6619 -- 142 2649 0.206 0.2537 0.0 100.0
X Ray Diffraction 2.6619 2.9297 -- 156 2659 0.2188 0.2531 0.0 100.0
X Ray Diffraction 2.9297 3.3535 -- 140 2664 0.2054 0.2529 0.0 100.0
X Ray Diffraction 3.3535 4.2246 -- 148 2714 0.1927 0.2076 0.0 100.0
X Ray Diffraction 4.2246 44.7085 -- 163 2819 0.1914 0.2265 0.0 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.3501
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_bond_d 0.008
f_dihedral_angle_d 15.733
f_chiral_restr 0.06
f_angle_d 1.034
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1945
Nucleic Acid Atoms 334
Heterogen Atoms 0
Solvent Atoms 274

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.22
MOLREP phasing
PHENIX refinement version: 1.10.1_2155
PDB_EXTRACT data extraction version: 3.22
MOSFLM data reduction