X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.3
Temperature 289.0
Details PEG4000, AMMONIUM ACETATE, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.91 α = 90
b = 70.91 β = 90
c = 177.66 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
3 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 1999-04-28
CCD ADSC QUANTUM 4 -- 1999-05-01
CCD BRANDEIS - B2 -- 1999-05-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12C 0.93 NSLS X12C
SYNCHROTRON NSLS BEAMLINE X26C 1.1 NSLS X26C
ROTATING ANODE HOME SOURCE 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 30 -- -- -- -- -- -- n/a -- -- 5.0

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
-- 2.03 29.87 -- 0.0 -- 26048 2339 86.6 -- 0.209 0.209 0.262 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 2.03 2.16 -- 214 2259 0.274 0.312 0.021 50.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 24.2
Anisotropic B[1][1] 1.46
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.46
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.91
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 3.36
x_mcbond_it 1.26
x_scbond_it 2.23
x_mcangle_it 2.03
x_angle_deg 1.3
x_improper_angle_d 0.71
x_bond_d 0.008
x_dihedral_angle_d 27.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.25
Luzzati Sigma A (Observed) 0.31
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.32
Luzzati Sigma A (R-Free Set) 0.27
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2496
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 149

Software

Software
Software Name Purpose
PHASES phasing
X-PLOR refinement version: 3.851
DENZO data reduction
SCALEPACK data scaling