X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.8
Temperature 293.0
Details 0.2 M potassium sodium tartarate tetrahydrate, 20% (w/v) PEG 3350, pH 7.8, vapor diffusion, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.34 α = 90
b = 70.34 β = 90
c = 74.84 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2012-02-25
Diffraction Radiation
Monochromator Protocol
-- Single Wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-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
1.1 51.26 100.0 0.042 -- -- 8.3 76552 76552 0.0 -3.0 --
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)
1.1 1.12 100.0 0.755 -- 2.9 8.2 3745

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 1.1 33.036 -- 1.72 -- 76478 3844 99.95 -- 0.1391 0.1387 0.146 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 1.1 1.1139 -- 134 2651 0.2011 0.2149 -- 100.0
X Ray Diffraction 1.1139 1.1286 -- 130 2652 0.1852 0.1948 -- 100.0
X Ray Diffraction 1.1286 1.1441 -- 148 2640 0.1639 0.194 -- 100.0
X Ray Diffraction 1.1441 1.1604 -- 153 2631 0.1576 0.1621 -- 100.0
X Ray Diffraction 1.1604 1.1777 -- 134 2676 0.1414 0.1631 -- 100.0
X Ray Diffraction 1.1777 1.1961 -- 121 2679 0.1424 0.155 -- 100.0
X Ray Diffraction 1.1961 1.2157 -- 145 2658 0.1354 0.1586 -- 100.0
X Ray Diffraction 1.2157 1.2367 -- 145 2652 0.1325 0.1433 -- 100.0
X Ray Diffraction 1.2367 1.2592 -- 142 2662 0.1233 0.1331 -- 100.0
X Ray Diffraction 1.2592 1.2834 -- 133 2668 0.1228 0.1587 -- 100.0
X Ray Diffraction 1.2834 1.3096 -- 148 2662 0.1144 0.1325 -- 100.0
X Ray Diffraction 1.3096 1.3381 -- 130 2659 0.1073 0.1431 -- 100.0
X Ray Diffraction 1.3381 1.3692 -- 138 2678 0.1067 0.1322 -- 100.0
X Ray Diffraction 1.3692 1.4034 -- 146 2675 0.1066 0.1337 -- 100.0
X Ray Diffraction 1.4034 1.4414 -- 147 2660 0.1029 0.1181 -- 100.0
X Ray Diffraction 1.4414 1.4838 -- 141 2676 0.0997 0.1354 -- 100.0
X Ray Diffraction 1.4838 1.5317 -- 155 2696 0.1003 0.1184 -- 100.0
X Ray Diffraction 1.5317 1.5864 -- 140 2671 0.0991 0.1085 -- 100.0
X Ray Diffraction 1.5864 1.65 -- 141 2674 0.1062 0.1083 -- 100.0
X Ray Diffraction 1.65 1.7251 -- 145 2703 0.1118 0.1247 -- 100.0
X Ray Diffraction 1.7251 1.816 -- 137 2706 0.1186 0.1328 -- 100.0
X Ray Diffraction 1.816 1.9298 -- 144 2692 0.1249 0.1305 -- 100.0
X Ray Diffraction 1.9298 2.0787 -- 163 2716 0.1275 0.1342 -- 100.0
X Ray Diffraction 2.0787 2.2879 -- 148 2720 0.1334 0.1428 -- 100.0
X Ray Diffraction 2.2879 2.6188 -- 135 2764 0.1494 0.1768 -- 100.0
X Ray Diffraction 2.6188 3.299 -- 166 2763 0.1712 0.1455 -- 100.0
X Ray Diffraction 3.299 33.051 -- 135 2950 0.1617 0.1676 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.9167
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.08
f_plane_restr 0.009
f_chiral_restr 0.092
f_angle_d 1.214
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1381
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 220

Software

Computing
Computing Package Purpose
JDIRECTOR Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: dev_1131) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
SCALA version: 0.1.27 data reduction
Mosflm data collection