X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 277.0
Details 20% Isopropanol 0.1M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.71 α = 90
b = 97.71 β = 90
c = 80.58 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 2008-03-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5 -- --

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
2.3 36.37 97.7 0.079 0.076 -- 3.8 19531 19082 -- -- --
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)
2.3 2.38 100.0 0.446 0.446 2.1 3.8 1950

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 2.3 36.37 -- 0.0 19492 19034 942 97.65 0.172 0.172 0.169 0.233 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 2.3 2.361 -- 62 1367 0.252 0.329 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.092
Anisotropic B[1][1] 1.91
Anisotropic B[1][2] 0.95
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.91
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.86
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.001
r_mcbond_other 1.227
r_angle_refined_deg 1.641
r_dihedral_angle_1_deg 5.812
r_mcangle_it 5.883
r_gen_planes_refined 0.007
r_bond_refined_d 0.015
r_mcbond_it 3.955
r_scbond_it 9.264
r_angle_other_deg 0.957
r_dihedral_angle_3_deg 15.273
r_dihedral_angle_4_deg 13.908
r_chiral_restr 0.088
r_gen_planes_other 0.001
r_scangle_it 11.261
r_dihedral_angle_2_deg 33.496
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2216
Nucleic Acid Atoms 0
Heterogen Atoms 22
Solvent Atoms 147

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing version: 2.1.2
REFMAC refinement
PDB_EXTRACT data extraction version: 3.100
CrystalClear data collection
HKL-2000 data reduction
HKL-2000 data scaling