X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 293.0
Details 0.1M potassium thiocianate, 30% PEG 2000, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.71 α = 99.95
b = 69.7 β = 111.04
c = 72.38 γ = 110.48
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 2008-01-07
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE -- 1.514 -- --

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
2.5 50 95.0 0.094 -- -- 2.6 32162 30549 0.0 0.0 20.343
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)
2.5 2.6 93.9 0.273 -- 5.0 2.6 --

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 2.5 15.0 -- 0.0 -- 30430 3069 95.38 -- 0.227 0.22 0.286 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 2.5 2.585 -- 315 2533 0.239 0.339 -- 93.96
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.635
Anisotropic B[1][1] -0.36
Anisotropic B[1][2] 0.25
Anisotropic B[1][3] 0.29
Anisotropic B[2][2] 0.26
Anisotropic B[2][3] -0.49
Anisotropic B[3][3] 0.31
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.663
r_scbond_it 1.114
r_mcangle_it 1.601
r_mcbond_it 0.915
r_symmetry_hbond_refined 0.402
r_bond_refined_d 0.011
r_angle_refined_deg 1.422
r_dihedral_angle_1_deg 6.916
r_dihedral_angle_2_deg 35.26
r_dihedral_angle_3_deg 21.113
r_dihedral_angle_4_deg 20.588
r_chiral_restr 0.094
r_gen_planes_refined 0.005
r_nbd_refined 0.274
r_nbtor_refined 0.33
r_xyhbond_nbd_refined 0.24
r_symmetry_vdw_refined 0.342
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6288
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 32

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.005 data extraction
REFMAC5 refinement
Phaser molecular replacement
Xscale data processing