X-RAY DIFFRACTION Experimental Data & Validation

X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9.5
Temperature 289.0
Details 20% PEG8000, 0.1M CHES pH9.5. Cryo protected with 25% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.85 α = 90
b = 121.67 β = 96.65
c = 64.55 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 RIGAKU SATURN 944+ -- 2011-01-23
Diffraction Radiation
Monochromator Protocol
Varimax SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418 -- --

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 64.12 96.9 0.063 -- -- -- -- 47423 -- -3.0 18.605
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 2.05 76.0 0.174 -- 5.92 -- --

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 19.97 -- 0.0 -- 46990 2371 95.05 -- 0.1521 0.1497 0.1954 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 -- 156 3073 0.143 0.207 -- 89.77
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.9431
Anisotropic B[1][1] -0.63
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.03
Anisotropic B[2][2] 1.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.74
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 1.876
r_mcbond_other 0.15
r_gen_planes_refined 0.005
r_gen_planes_other 0.001
r_angle_refined_deg 1.276
r_bond_refined_d 0.012
r_bond_other_d 0.001
r_scangle_it 3.176
r_angle_other_deg 0.904
r_chiral_restr 0.078
r_dihedral_angle_1_deg 6.597
r_mcangle_it 1.099
r_dihedral_angle_4_deg 20.079
r_dihedral_angle_3_deg 12.201
r_dihedral_angle_2_deg 31.838
r_mcbond_it 0.604
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5377
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 521

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing version: 2.1.4
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10