X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 295.0
Details PEG 8K, L-homoserine, 3-aminopyridine dinucleotide, sodium cacodylate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.78 α = 90
b = 104.09 β = 91.93
c = 120.64 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 218
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS II -- 1996-02-22
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
2.6 40 99.2 0.081 -- -- 3.7 44409 164716 3.0 0.0 35.4
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)
2.6 2.69 98.1 0.344 -- -- 3.5 4392

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
-- 2.6 39.4 0.0 2.0 44409 44116 3998 98.5 0.217 0.215 0.215 0.283 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 2.6 2.76 -- 659 6567 0.3 0.405 0.016 97.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 28.6
Anisotropic B[1][1] 1.8
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 8.79
Anisotropic B[2][2] 0.66
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.46
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.5
c_dihedral_angle_d 23.3
c_mcangle_it 5.83
c_scbond_it 6.43
c_bond_d 0.008
c_scangle_it 8.06
c_improper_angle_d 1.01
c_mcbond_it 4.05
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.32
Luzzati Sigma A (Observed) 0.31
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.44
Luzzati Sigma A (R-Free Set) 0.52
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10840
Nucleic Acid Atoms 956
Heterogen Atoms 55
Solvent Atoms 352

Software

Software
Software Name Purpose
CNS refinement
DENZO data reduction
SCALEPACK data scaling
CNS phasing