X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.5
Temperature 293.0
Details 0.5M LiCl, 0.1M Tris-HCl pH 8.5, 28% PEG 6000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.73 α = 90
b = 54.34 β = 108.61
c = 66.77 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2009-03-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00000 Photon Factory BL-5A

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
2.2 50 99.8 0.17 -- -- 3.7 -- 15196 -- -- --
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)
2.2 2.28 100.0 0.614 -- -- 3.7 --

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 2.2 50.0 -- -- -- 14420 762 99.7 -- 0.1874 0.18451 0.2399 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 2.201 2.258 -- 51 1062 0.266 0.271 -- 99.55
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.867
Anisotropic B[1][1] -0.68
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.6
Anisotropic B[2][2] 0.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.61
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.898
r_gen_planes_refined 0.007
r_dihedral_angle_3_deg 15.928
r_dihedral_angle_4_deg 15.942
r_bond_refined_d 0.014
r_scbond_other 2.744
r_angle_other_deg 1.027
r_scbond_it 2.745
r_long_range_B_refined 6.294
r_long_range_B_other 6.293
r_mcbond_it 2.094
r_mcbond_other 2.083
r_dihedral_angle_2_deg 35.225
r_mcangle_other 3.276
r_mcangle_it 3.273
r_bond_other_d 0.002
r_gen_planes_other 0.002
r_angle_refined_deg 1.72
r_chiral_restr 0.107
r_scangle_other 4.412
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2117
Nucleic Acid Atoms 0
Heterogen Atoms 37
Solvent Atoms 187

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0135
HKL-2000 data reduction
HKL-2000 data scaling
MOLREP phasing version: 10.2.12
PDB_EXTRACT data extraction version: 3.24