X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details ammonium sulfate, sodium chloride, MES buffer, NAD+, UDP-glucose, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 160.24 α = 90
b = 160.24 β = 90
c = 99.27 γ = 90
Symmetry
Space Group I 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD CUSTOM-MADE -- 1999-08-23
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSING SI (111) DOUBLE CRYSTAL MONOCHROMATOR AND VERTICALLY FOCUSING MIRROR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID -- 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
1.14 99 86.4 0.097 -- -- 5.9 -- 196326 -- -3.0 11.59
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)
1.14 1.19 38.0 0.366 -- 1.7 1.4 --

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 1.2 20.0 -- 0.0 -- 184009 9260 92.3 -- 0.192 0.192 0.198 REFLECTIONS FOR CROSS-VALIDATION WERE SELECTED FROM A STANDARD SET OF DUMMY DATA GENERATED USING THE CCP4 SUITE, WHERE 5% OF THE RELECTIONS ARE FLAGGED. THE SELECTED REFLECTIONS MATCH THOSE IN PDB ENTRY 1QRR.
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 1.2 1.24 -- 806 14360 0.2813 0.2984 -- 82.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 13.43
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 1.983
c_scbond_it 1.361
c_mcangle_it 1.117
c_mcbond_it 0.798
c_improper_angle_d 1.11
c_bond_d 0.012
c_angle_deg 1.58
c_dihedral_angle_d 22.74
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.14
Luzzati Sigma A (Observed) 0.1
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.15
Luzzati Sigma A (R-Free Set) 0.1
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3032
Nucleic Acid Atoms 0
Heterogen Atoms 90
Solvent Atoms 386

Software

Computing
Computing Package Purpose
D*TREK, HKL-2000 Data Reduction (intensity integration)
SCALEPACK, CCP4 (TRUNCATE) Data Reduction (data scaling)
CNS 0.9A Structure Solution
CNS 0.9A Structure Refinement
Software
Software Name Purpose
CNS version: 0.9A refinement
CNS version: 0.9A model building
TRUNCATE data reduction
SCALEPACK data reduction
HKL2000 data collection
D*TREK data collection