X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 277.0
Details 5.00% polyethylene glycol 6000, 0.1M TRIS pH 8.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75 α = 90
b = 75 β = 90
c = 74.9 γ = 120
Symmetry
Space Group P 31 2 1

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 2014-12-06
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 -- 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
1.23 29.8 98.3 -- 0.115 3.912 6.9 69760 69760 -- -- --
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)
1.23 1.26 86.1 0.804 0.804 0.9 4.1 4473

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 1.23 29.796 -- 0.0 -- 69700 3374 98.23 -- 0.1172 0.1164 0.1339 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 1.23 1.262 -- 192 4272 0.287 0.293 -- 85.71
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.4434
Anisotropic B[1][1] 0.2
Anisotropic B[1][2] 0.1
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.2
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.64
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 19.353
r_gen_planes_other 0.004
r_sphericity_bonded 8.773
r_dihedral_angle_2_deg 36.157
r_mcbond_it 2.064
r_dihedral_angle_3_deg 11.474
r_sphericity_free 30.129
r_mcbond_other 1.992
r_gen_planes_refined 0.009
r_angle_other_deg 1.091
r_angle_refined_deg 1.697
r_chiral_restr 0.104
r_bond_other_d 0.003
r_rigid_bond_restr 2.717
r_dihedral_angle_1_deg 6.157
r_bond_refined_d 0.016
r_mcangle_it 2.034
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1396
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 198

Software

Software
Software Name Purpose
PDB_EXTRACT data extraction version: 3.10
SOLVE phasing
SCALA data scaling version: 3.3.20
REFMAC refinement version: 5.8.0103
MOSFLM data reduction