X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 298.0
Details PEG 4000, NaCl, MgCl2, MES, pH 6.2, VAPOR DIFFUSION, HANGING DROP at 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.3 α = 90
b = 86.3 β = 90
c = 133 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 125
2 125
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- 1999-05-23
CCD ADSC QUANTUM 4 -- 2000-03-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --
SYNCHROTRON NSLS BEAMLINE X4A -- NSLS X4A

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
2.35 20 99.9 0.081 -- -- 4.2 45864 45805 -- -3.0 24.7
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)
2.35 2.43 99.8 0.345 -- -- 4.0 4571

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
-- 2.35 20.0 -- 2.0 46014 38060 3849 82.6 0.25 0.215 0.21 0.256 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 2.35 2.5 -- 528 4274 0.331 0.362 0.016 62.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 41.4
RMS Deviations
Key Refinement Restraint Deviation
x_mcbond_it 2.81
x_angle_deg 1.1
x_improper_angle_deg 1.16
x_scbond_it 4.63
x_bond_d 0.007
x_mcangle_it 4.5
x_dihedral_angle_deg 23.8
x_scangle_it 7.03
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.31
Luzzati Sigma A (Observed) 0.41
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.37
Luzzati Sigma A (R-Free Set) 0.44
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3294
Nucleic Acid Atoms 1704
Heterogen Atoms 12
Solvent Atoms 319

Software

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