X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 298.0
Details 0.2M lithium sulphate, 0.1M Tris, 30% w/v PEG 4K, pH 8.5, NAD+ (0.09mM)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 133.63 α = 90
b = 277.72 β = 90
c = 56 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM -- 2011-02-03
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9334 ESRF ID14-4

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 48.14 99.2 0.12 -- -- 6.7 -- 93173 -- -- --
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 2.42 95.3 0.276 -- 2.7 4.6 --

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 48.143 -- 0.0 -- 88435 4653 99.17 -- 0.1775 0.174 0.2438 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 2.36 -- 295 6058 0.216 0.31 -- 93.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.09
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.04
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 1.592
r_mcbond_other 1.59
r_bond_other_d 0.001
r_dihedral_angle_1_deg 6.958
r_bond_refined_d 0.014
r_dihedral_angle_2_deg 36.443
r_gen_planes_other 0.001
r_angle_other_deg 0.874
r_dihedral_angle_3_deg 16.369
r_gen_planes_refined 0.007
r_mcangle_it 2.554
r_dihedral_angle_4_deg 18.153
r_angle_refined_deg 1.713
r_chiral_restr 0.095
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14974
Nucleic Acid Atoms 0
Heterogen Atoms 325
Solvent Atoms 928

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.9
REFMAC refinement version: 5.7.0032
PDB_EXTRACT data extraction version: 3.20
iMOSFLM data reduction
MOLREP phasing