X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 277.0
Details 11% PEG 4000, 0.1M HEPES, 10% isopropanol, 6.5mM Man9, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.14 α = 90
b = 106.02 β = 90
c = 145.31 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2011-05-13
Diffraction Radiation
Monochromator Protocol
Liquid nitrogen-cooled double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2

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
1.29 25 99.9 -- 0.077 -- 6.5 139537 139361 0.0 0.0 14.0
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)
1.29 1.32 99.9 -- 0.546 3.27 6.4 10219

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 1.29 24.899 -- 1.35 139537 139213 1643 99.82 -- 0.1593 0.159 0.1838 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 1.29 1.328 -- 136 11330 0.1521 0.1773 -- 100.0
X Ray Diffraction 1.328 1.3708 -- 135 11394 0.1375 0.19 -- 100.0
X Ray Diffraction 1.3708 1.4198 -- 137 11357 0.1279 0.1688 -- 100.0
X Ray Diffraction 1.4198 1.4767 -- 135 11391 0.1216 0.1561 -- 100.0
X Ray Diffraction 1.4767 1.5438 -- 137 11417 0.1106 0.1437 -- 100.0
X Ray Diffraction 1.5438 1.6252 -- 136 11426 0.1105 0.1456 -- 100.0
X Ray Diffraction 1.6252 1.727 -- 136 11456 0.115 0.1608 -- 100.0
X Ray Diffraction 1.727 1.8603 -- 137 11432 0.1275 0.1472 -- 100.0
X Ray Diffraction 1.8603 2.0475 -- 137 11469 0.1388 0.174 -- 100.0
X Ray Diffraction 2.0475 2.3435 -- 138 11514 0.1596 0.1617 -- 100.0
X Ray Diffraction 2.3435 2.9519 -- 138 11599 0.1827 0.1985 -- 100.0
X Ray Diffraction 2.9519 24.9039 -- 141 11785 0.1868 0.2172 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ANISOTROPIC
Mean Isotropic B 20.6
Anisotropic B[1][1] -1.381
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.4263
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.0453
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.074
f_dihedral_angle_d 20.297
f_plane_restr 0.006
f_bond_d 0.007
f_angle_d 1.273
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.15
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3263
Nucleic Acid Atoms 0
Heterogen Atoms 131
Solvent Atoms 306

Software

Software
Software Name Purpose
Blu-Ice data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.7.2_865)
XDS data reduction
XSCALE data scaling