X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 277.0
Details 0.1M potassium chloride, 15.0% polyethylene glycol monomethyl ether 5000, 0.1M HEPES pH 7.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 127.28 α = 90
b = 127.28 β = 90
c = 78.86 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Vertical focusing mirror; double crystal Si(111) monochromator 2013-11-15
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 1.0 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
2.2 39.43 99.7 0.116 -- -- 3.809 -- 72455 -- -3.0 34.1
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)
2.2 2.26 98.0 0.83 -- 2.0 -- --

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 2.2 39.432 -- 0.0 -- 72263 3629 99.68 -- 0.1751 0.1744 0.1897 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 2.2 2.257 -- 253 4955 0.244 0.293 -- 98.3
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.3644
Anisotropic B[1][1] 8.73
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 8.73
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -17.47
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.011
r_gen_planes_other 0.009
r_dihedral_angle_3_deg 12.274
r_bond_refined_d 0.019
r_mcbond_other 2.28
r_dihedral_angle_1_deg 5.2
r_mcbond_it 2.282
r_bond_other_d 0.01
r_mcangle_it 3.713
r_chiral_restr 0.101
r_angle_other_deg 1.493
r_angle_refined_deg 1.635
r_dihedral_angle_4_deg 18.357
r_dihedral_angle_2_deg 35.92
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8553
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 518

Software

Software
Software Name Purpose
XDS data reduction
XSCALE data scaling
REFMAC refinement version: 5.8.0123
PHASER phasing