X-RAY DIFFRACTION Experimental Data & Validation

X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.3
Temperature 294.0
Details 15% PEG 3350, 0.05M magnesium chloride, 0.067M sodium chloride, 0.1M Tris, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.7 α = 90
b = 81.3 β = 110.07
c = 58.28 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2012-07-27
Diffraction Radiation
Monochromator Protocol
Side scattering bent cube I-beam single crystal, asymmetric cut 4.965 degs SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 1.0 SSRL BL11-1

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
2.3 50 93.33 -- 0.083 -- 6.6 20145 20145 1.0 1.0 40.05
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)
2.3 2.34 95.66 -- 0.715 2.13 6.8 --

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 2.3 46.198 -- 0.0 18852 18852 1852 87.34 0.2698 0.2698 0.265 0.3121 RANDOM
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 2.3 2.3559 -- 130 1203 0.3256 0.4225 -- 81.0
X Ray Diffraction 2.3559 2.4253 -- 146 1313 0.2961 0.3896 -- 88.0
X Ray Diffraction 2.4253 2.5035 -- 154 1315 0.2882 0.3398 -- 89.0
X Ray Diffraction 2.5035 2.593 -- 140 1345 0.2654 0.3306 -- 90.0
X Ray Diffraction 2.593 2.6968 -- 140 1324 0.2761 0.3578 -- 89.0
X Ray Diffraction 2.6968 2.8195 -- 128 1309 0.2757 0.3332 -- 87.0
X Ray Diffraction 2.8195 2.9682 -- 156 1391 0.2607 0.3433 -- 94.0
X Ray Diffraction 2.9682 3.1541 -- 156 1439 0.2597 0.3393 -- 96.0
X Ray Diffraction 3.1541 3.3975 -- 152 1399 0.2541 0.2852 -- 94.0
X Ray Diffraction 3.3975 3.7393 -- 139 1214 0.2547 0.3293 -- 82.0
X Ray Diffraction 3.7393 4.2801 -- 121 1089 0.2565 0.3144 -- 72.0
X Ray Diffraction 4.2801 5.3911 -- 134 1261 0.2449 0.2814 -- 83.0
X Ray Diffraction 5.3911 46.198 -- 156 1398 0.2735 0.2742 -- 91.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.6601
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 6.0033
Anisotropic B[2][2] 12.5216
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -11.8615
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.003
f_dihedral_angle_d 15.537
f_plane_restr 0.002
f_angle_d 0.565
f_chiral_restr 0.041
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3475
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 74

Software

Software
Software Name Purpose
Blue data collection version: ice
PHENIX model building version: (phenix.automr)
PHENIX refinement version: (phenix.refine: 1.7.1_743)
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing