X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.4
Temperature 295.0
Details Ammonium sulphate, Calcium chloride, NAD+, Sodium Acetate , pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.4 α = 90
b = 80.4 β = 90
c = 250.16 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 218
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS II -- 1997-01-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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
2.3 38 98.4 0.077 -- -- 5.4 36978 188533 0.0 3.0 17.6
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)
2.3 2.38 94.8 0.49 -- -- 4.0 3445

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
-- 2.3 35.96 0.0 2.0 35733 32162 2232 85.7 0.234 0.218 0.218 0.269 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 2.3 2.44 -- 270 3642 0.227 0.283 0.017 64.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 27.5
Anisotropic B[1][1] 1.19
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.19
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.38
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 1.62
c_angle_deg 1.4
c_dihedral_angle_d 23.1
c_mcangle_it 1.87
c_improper_angle_d 0.91
c_scangle_it 2.34
c_mcbond_it 1.13
c_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.21
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.36
Luzzati Sigma A (R-Free Set) 0.29
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5420
Nucleic Acid Atoms 5717
Heterogen Atoms 46
Solvent Atoms 253

Software

Software
Software Name Purpose
SOLVE/SHARP/GHKL/CCP4/DM/CNS model building
CNS refinement version: 0.9
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing
SHARP phasing
GHKL phasing
CCP4 phasing
DM phasing
CNS phasing