X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details PEG 3350, pH 7.5, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.43 α = 90
b = 66.83 β = 90
c = 72.49 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2006-06-24
Diffraction Radiation
Monochromator Protocol
Ni filter SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 1.00 APS 21-ID-D

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 30 85.3 0.094 -- -- 6.4 18358 17278 2.0 2.0 --
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)
2.0 2.07 -- 0.587 -- 1.8 4.1 --

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 2.0 30.0 -- -- -- 16921 1320 95.49 -- 0.19616 0.1928 0.24263 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 2.0 2.052 -- 82 910 0.251 0.325 -- 72.46
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.32
Anisotropic B[1][1] 2.39
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.66
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.73
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_other 0.559
r_angle_other_deg 0.911
r_dihedral_angle_3_deg 12.522
r_bond_other_d 0.001
r_dihedral_angle_2_deg 32.871
r_gen_planes_other 0.001
r_chiral_restr 0.088
r_scangle_it 5.028
r_mcbond_it 1.61
r_sphericity_bonded 3.773
r_gen_planes_refined 0.007
r_dihedral_angle_4_deg 13.11
r_rigid_bond_restr 2.193
r_sphericity_free 12.235
r_angle_refined_deg 1.396
r_dihedral_angle_1_deg 3.849
r_scbond_it 3.433
r_bond_refined_d 0.018
r_mcangle_it 2.772
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2135
Nucleic Acid Atoms 0
Heterogen Atoms 21
Solvent Atoms 141

Software

Software
Software Name Purpose
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005
DENZO data reduction
SCALEPACK data scaling