X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.67
Temperature 293.0
Details 0.01M nickel (II) chloride, 22.0% polyethylene glycol monomethyl ether 2000, 0.2M NDSB-256, 0.1M TRIS pH 8.67, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 226.44 α = 90
b = 67.68 β = 90
c = 90.07 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2013-08-01
Diffraction Radiation
Monochromator Protocol
single crystal Si(111) bent MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.9792, 0.97868 SSRL BL11-1

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
1.8 29.21 95.4 0.075 -- -- 3.74 -- 127394 -- -3.0 21.082
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 1.86 89.8 0.563 -- 1.5 -- --

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
MAD 1.8 29.211 -- 0.0 -- 127320 6400 98.67 -- 0.1516 0.1501 0.1796 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 -- 459 8834 0.256 0.282 -- 98.62
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.3603
Anisotropic B[1][1] -1.19
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.57
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.38
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 2.577
r_dihedral_angle_3_deg 11.19
r_gen_planes_refined 0.009
r_gen_planes_other 0.004
r_mcangle_it 3.392
r_bond_refined_d 0.015
r_chiral_restr 0.102
r_angle_refined_deg 1.6
r_dihedral_angle_4_deg 15.522
r_mcbond_other 2.568
r_dihedral_angle_2_deg 33.28
r_angle_other_deg 1.121
r_bond_other_d 0.005
r_dihedral_angle_1_deg 6.675
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8344
Nucleic Acid Atoms 0
Heterogen Atoms 60
Solvent Atoms 1264

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PDB_EXTRACT data extraction version: 3.10
SHELX phasing
SHARP phasing
XSCALE data scaling
REFMAC refinement version: 5.7.0032
XDS data reduction
SHELXD phasing