X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details PEG 4000, sodium acetate, mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 94.87 α = 90
b = 123.46 β = 90
c = 133.89 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD CUSTOM-MADE -- 1999-09-21
CCD CUSTOM-MADE -- 2000-05-25
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97921,0.97935,1.016273 APS 19-ID
SYNCHROTRON APS BEAMLINE 19-ID 0.99187 APS 19-ID

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 98.8 0.073 -- -- 7.0 53318 52782 0.0 -3.0 23.7
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)
2.0 2.07 99.1 0.415 -- 4.0 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
MAD 2.0 23.81 0.0 0.0 53318 51168 2585 95.9 -- 0.203 0.203 0.23 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 2.07 -- 280 4686 0.237 0.255 0.015 94.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 32.3
Anisotropic B[1][1] 5.92
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.58
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.5
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.013
c_scbond_it 2.95
c_dihedral_angle_d 21.6
c_angle_deg 1.7
c_mcbond_it 1.86
c_improper_angle_d 1.72
c_scangle_it 4.52
c_mcangle_it 2.78
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Luzzati Sigma A (Observed) 0.13
Luzzati Resolution Cutoff (Low) 25.0
Luzzati ESD (R-Free Set) 0.27
Luzzati Sigma A (R-Free Set) 0.17
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3926
Nucleic Acid Atoms 0
Heterogen Atoms 96
Solvent Atoms 421

Software

Software
Software Name Purpose
DTCOLLECT data collection
HKL-2000 data reduction
SOLVE phasing
SHARP phasing
O model building
CNS refinement version: 0.9
DTCOLLECT data reduction
HKL-2000 data scaling