X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.6
Temperature 292.0
Details 2mM NAD+, 16mM Spermine, 14% Polyethelene Glycol Monomethyl Ether 2000, 12mM Sodium Potassium Tartrate, 100mM Tris pH 8.6, 0.1mM DTT, 0.007% Sodium Azide, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.17 α = 79.34
b = 86.33 β = 78.66
c = 125.7 γ = 71.58
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ Osmic-Blue confocal optics 2001-11-27
Diffraction Radiation
Monochromator Protocol
Osmic Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 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
2.3 20 96.4 -- 0.108 -- 3.4 123136 123136 0.0 -3.0 19.5
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 2.34 94.2 -- 0.463 2.8 3.3 6019

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 2.3 19.99 -3.0 0.0 123136 123017 12264 96.4 -- -- 0.229 0.246 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 2.38 -- 1200 10800 0.299 0.307 0.009 94.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 31.3
Anisotropic B[1][1] 4.49
Anisotropic B[1][2] -4.99
Anisotropic B[1][3] 0.21
Anisotropic B[2][2] -0.85
Anisotropic B[2][3] 2.01
Anisotropic B[3][3] -3.64
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.94
c_scbond_it 1.97
c_mcangle_it 1.94
c_mcbond_it 1.19
c_improper_angle_d 1.19
c_bond_d 0.008
c_angle_deg 1.5
c_dihedral_angle_d 24.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.31
Luzzati Sigma A (Observed) 0.33
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.34
Luzzati Sigma A (R-Free Set) 0.34
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 20120
Nucleic Acid Atoms 0
Heterogen Atoms 416
Solvent Atoms 1044

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE, MOLREP Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
MolRep model building
AMORE model building
SCALEPACK data reduction
DENZO data collection