X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details 100 mM Tris-HCl, 150 mM magnesium chloride hexahydrate, 25% PEG4000, 6% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.07 α = 90
b = 152.63 β = 90
c = 173.76 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD flat collimating Rh coated mirror, toroidal focusing mirror 2013-01-01
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL14-1 1.24 SSRL BL14-1

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
2.5 39.11 99.3 -- -- -- 7.0 79881 79261 -- -- --
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)
2.5 2.63 95.6 -- -- -- 5.8 --

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 2.5 39.108 -- 1.34 -- 79236 3978 99.2 -- 0.1918 0.189 0.2451 --
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 2.4998 2.5302 -- 126 2184 0.2556 0.3295 -- 82.0
X Ray Diffraction 2.5302 2.5623 -- 132 2644 0.2588 0.3493 -- 100.0
X Ray Diffraction 2.5623 2.596 -- 121 2721 0.2648 0.3555 -- 100.0
X Ray Diffraction 2.596 2.6315 -- 138 2652 0.2553 0.3401 -- 100.0
X Ray Diffraction 2.6315 2.6691 -- 142 2674 0.2428 0.304 -- 100.0
X Ray Diffraction 2.6691 2.7089 -- 130 2693 0.2216 0.296 -- 100.0
X Ray Diffraction 2.7089 2.7513 -- 133 2677 0.2166 0.2894 -- 100.0
X Ray Diffraction 2.7513 2.7964 -- 142 2685 0.2124 0.326 -- 100.0
X Ray Diffraction 2.7964 2.8446 -- 140 2656 0.2232 0.2771 -- 100.0
X Ray Diffraction 2.8446 2.8963 -- 159 2686 0.2244 0.3149 -- 100.0
X Ray Diffraction 2.8963 2.952 -- 142 2665 0.2193 0.3041 -- 100.0
X Ray Diffraction 2.952 3.0122 -- 138 2696 0.2213 0.3045 -- 100.0
X Ray Diffraction 3.0122 3.0777 -- 151 2701 0.2087 0.2836 -- 100.0
X Ray Diffraction 3.0777 3.1492 -- 116 2678 0.206 0.3013 -- 100.0
X Ray Diffraction 3.1492 3.228 -- 147 2696 0.2006 0.2675 -- 100.0
X Ray Diffraction 3.228 3.3152 -- 147 2712 0.1935 0.2848 -- 100.0
X Ray Diffraction 3.3152 3.4127 -- 153 2683 0.1875 0.256 -- 100.0
X Ray Diffraction 3.4127 3.5228 -- 163 2668 0.1843 0.2383 -- 100.0
X Ray Diffraction 3.5228 3.6486 -- 157 2702 0.1804 0.2544 -- 100.0
X Ray Diffraction 3.6486 3.7946 -- 150 2699 0.1774 0.2361 -- 100.0
X Ray Diffraction 3.7946 3.9671 -- 138 2703 0.1708 0.2341 -- 100.0
X Ray Diffraction 3.9671 4.176 -- 141 2723 0.1701 0.2144 -- 100.0
X Ray Diffraction 4.176 4.4373 -- 133 2730 0.1656 0.2316 -- 100.0
X Ray Diffraction 4.4373 4.7794 -- 137 2745 0.1621 0.2146 -- 100.0
X Ray Diffraction 4.7794 5.2593 -- 147 2743 0.1733 0.2196 -- 100.0
X Ray Diffraction 5.2593 6.018 -- 143 2759 0.2052 0.2504 -- 100.0
X Ray Diffraction 6.018 7.573 -- 154 2780 0.2038 0.2564 -- 100.0
X Ray Diffraction 7.573 39.1129 -- 158 2903 0.1607 0.1726 -- 99.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_dihedral_angle_d 15.575
f_chiral_restr 0.061
f_bond_d 0.008
f_angle_d 1.185
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14852
Nucleic Acid Atoms 0
Heterogen Atoms 264
Solvent Atoms 87

Software

Software
Software Name Purpose
Blu-Ice data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.8.2_1309)
XDS data reduction
SCALA data scaling