X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 1.6 M Potassium Phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 83.47 α = 90
b = 83.47 β = 90
c = 215.45 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M SILICON OPTICS 2007-08-19
Diffraction Radiation
Monochromator Protocol
double bounce Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 1.0,1.7368 SLS X06SA

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
1.8 40 98.4 0.075 -- -- 4.5 78209 78209 2.0 2.0 35.16
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)
1.8 1.91 96.0 0.351 -- 2.5 3.1 10654

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
SAD 1.8 15.0 2.0 2.0 78122 74151 3898 98.06 0.2 0.201 0.19898 0.23823 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 1.8 1.847 -- 206 4143 0.326 0.367 -- 73.75
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.156
Anisotropic B[1][1] 0.34
Anisotropic B[1][2] 0.17
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.34
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.52
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.354
r_mcbond_it 0.946
r_xyhbond_nbd_refined 0.159
r_mcangle_it 1.468
r_scbond_it 2.727
r_bond_refined_d 0.015
r_gen_planes_refined 0.007
r_dihedral_angle_1_deg 5.729
r_dihedral_angle_3_deg 19.619
r_symmetry_vdw_refined 0.275
r_scangle_it 4.377
r_nbtor_refined 0.31
r_angle_refined_deg 1.784
r_dihedral_angle_2_deg 39.375
r_nbd_refined 0.205
r_dihedral_angle_4_deg 20.569
r_symmetry_hbond_refined 0.177
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4780
Nucleic Acid Atoms 0
Heterogen Atoms 72
Solvent Atoms 428

Software

Software
Software Name Purpose
XDS data scaling
SHARP phasing
REFMAC refinement version: 5.2.0019
XDS data reduction