X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 295.0
Details cacodylate, ammonium sulfate, PEG 3350, 3-aminopyridine adenine dinucleotide phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 298.93 α = 90
b = 94.83 β = 104.18
c = 79.61 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 1999-09-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R -- -- --

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
2.95 31.38 99.8 0.084 -- -- 13.1 598907 45732 -- 3.4 140.2
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)
2.95 3.06 99.0 0.358 -- 3.4 3.1 4492

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 2.95 31.38 0.0 0.0 45732 45528 2747 99.8 0.207 0.207 0.205 0.247 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 2.95 3.06 -- 272 4188 0.323 0.369 0.022 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 46.2
Anisotropic B[1][1] 11.16
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 4.93
Anisotropic B[2][2] -3.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.95
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 24.3
c_angle_deg 1.4
c_scbond_it 1.75
c_scangle_it 2.86
c_improper_angle_d 0.88
c_mcangle_it 2.35
c_bond_d 0.009
c_mcbond_it 1.33
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.33
Luzzati Sigma A (Observed) 0.45
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.41
Luzzati Sigma A (R-Free Set) 0.58
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12980
Nucleic Acid Atoms 0
Heterogen Atoms 396
Solvent Atoms 236

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CNS refinement version: 0.9
CNS phasing version: 0.9