X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.5
Temperature 298.0
Details Li2SO4, Tris-HCl, NiCl2, pH 8.5, VAPOR DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 114.34 α = 90
b = 114.34 β = 90
c = 123.87 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 300 mm plate -- 2008-07-15
Diffraction Radiation
Monochromator Protocol
DCM SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97934 CLSI 08ID-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
2.95 38.66 99.6 0.084 -- -- 19.7 -- 10632 -- -- --
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)
2.95 3.06 96.1 0.675 -- -- 10.7 984

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 3.0 38.66 -- 0.0 -- 10051 480 99.86 -- 0.227 0.224 0.288 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 3.0 3.078 -- 34 680 0.322 0.446 -- 99.44
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 57.243
Anisotropic B[1][1] -0.42
Anisotropic B[1][2] -0.21
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.63
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 42.792
r_dihedral_angle_4_deg 23.374
r_mcangle_it 2.332
r_dihedral_angle_3_deg 24.774
r_dihedral_angle_1_deg 12.169
r_scangle_it 5.533
r_chiral_restr 0.072
r_bond_refined_d 0.007
r_angle_refined_deg 1.064
r_mcbond_it 1.229
r_scbond_it 3.299
r_gen_planes_refined 0.016
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1730
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 6

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing version: 2.1.4
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling