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_scangle_it 2.34
c_scbond_it 1.62
c_mcangle_it 1.87
c_mcbond_it 1.13
c_improper_angle_d 0.91
c_bond_d 0.007
c_angle_deg 1.4
c_dihedral_angle_d 23.1
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 0
Heterogen Atoms 46
Solvent Atoms 253

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE, SHARP, GHKL, CCP4, DM, CNS Structure Solution
CNS 0.9 Structure Refinement
Software
Software Name Purpose
CNS version: 0.9 refinement
SOLVE/SHARP/GHKL/CCP4/DM/CNS model building