X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details 50mM HEPES, 17.5% MPD, 25mM MES, 10% glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 94.54 α = 90
b = 94.54 β = 90
c = 113 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN A200 -- 2010-11-24
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.000 SPring-8 BL26B1

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
2.17 20 99.9 0.048 -- -- 10.5 -- 31376 -- -3.0 42.762
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)
2.17 2.25 100.0 0.339 -- -- 10.9 3106

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 2.17 19.79 -- 0.0 -- 31226 1516 99.57 -- 0.2006 0.1993 0.2271 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 2.17 2.226 -- 101 2139 0.221 0.271 -- 99.47
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.1839
Anisotropic B[1][1] 0.11
Anisotropic B[1][2] 0.06
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.17
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 1.703
r_scangle_it 2.685
r_angle_refined_deg 1.25
r_dihedral_angle_3_deg 14.821
r_mcangle_it 1.177
r_bond_refined_d 0.012
r_dihedral_angle_2_deg 32.234
r_mcbond_it 0.641
r_dihedral_angle_4_deg 18.423
r_chiral_restr 0.084
r_gen_planes_refined 0.006
r_dihedral_angle_1_deg 5.539
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3218
Nucleic Acid Atoms 0
Heterogen Atoms 51
Solvent Atoms 81

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10