X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 281.0
Details PEG 4000, glycerol, HEPES, sodium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.08 α = 90
b = 129.99 β = 111.22
c = 71.41 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
IMAGE PLATE RIGAKU RAXIS IV Yale Mirrors 1998-08-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 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
2.1 66.57 85.3 0.079 -- -- 1.43 48271 45724 3.0 1.0 1.9
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)
2.1 2.23 67.2 0.28 -- -- 1.4 5970

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
Difference Fourier Analysis 2.1 66.57 0.0 0.0 48271 45725 3703 85.3 -- -- 0.248 0.311 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 2.1 2.23 -- 497 5474 0.325 0.414 0.019 67.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 15.0
Anisotropic B[1][1] 4.87
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.24
Anisotropic B[2][2] -5.67
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.8
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.61
c_bond_d 0.015
c_angle_deg 1.4
c_dihedral_angle_d 20.8
c_scbond_it 2.86
c_mcbond_it 2.08
c_mcangle_it 2.96
c_improper_angle_d 1.24
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.29
Luzzati Sigma A (Observed) 0.35
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.4
Luzzati Sigma A (R-Free Set) 0.47
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7564
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 427

Software

Software
Software Name Purpose
X-PLOR model building
X-PLOR refinement version: 3.843
DENZO data reduction
SCALEPACK data scaling
X-PLOR phasing