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 = 159.68 α = 90
b = 159.68 β = 90
c = 99.04 γ = 90
Symmetry
Space Group I 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 105
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ Osmic Max-Flux confocal, multilayer mirrors 2000-01-31
Diffraction Radiation
Monochromator Protocol
Osmic Max-Flux confocal, multilayer mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200H 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
1.6 30 98.8 0.094 -- -- 4.42 -- 82759 -- -3.0 15.24
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)
1.6 1.66 97.6 0.362 -- 1.5 2.1 --

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 1.6 30.0 0.0 0.0 82704 82704 4125 98.8 -- -- 0.177 0.185 R-free flags were assigned using the CCP4 suite, based on a standard set of flags used for all SQD1 structural refinements.
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 1.6 1.66 8040 421 7619 0.2914 0.3043 -- 97.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 17.7
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 1.012
c_scbond_it 0.661
c_mcangle_it 0.69
c_mcbond_it 0.409
c_improper_angle_d 0.76
c_dihedral_angle_d 22.09
c_angle_deg 1.29
c_bond_d 0.0053
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.17
Luzzati Sigma A (Observed) 0.16
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.18
Luzzati Sigma A (R-Free Set) 0.16
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3033
Nucleic Acid Atoms 0
Heterogen Atoms 90
Solvent Atoms 398

Software

Computing
Computing Package Purpose
CRYSTALCLEAR (MSC/RIGAKU), DENZO Data Reduction (intensity integration)
SCALEPACK, CCP4 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
CCP4 data reduction
SCALEPACK data reduction
DENZO data collection
CRYSTALCLEAR data collection