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_mcangle_it 1.94
c_mcbond_it 1.19
c_scbond_it 1.97
c_improper_angle_d 1.19
c_angle_deg 1.5
c_bond_d 0.008
c_scangle_it 2.94
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

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
MOLREP phasing
CNS refinement version: 1.1