X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 293.0
Details 10mM NADP+ 25.5% of polyacrylic acid 0.1M Hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 94.17 α = 90
b = 120.28 β = 90
c = 151.11 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2009-07-17
Diffraction Radiation
Monochromator Protocol
Silicon 1 1 1 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2

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
2.8 94.11 97.2 0.129 0.129 -- 4.1 -- 41558 0.0 0.0 --
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)
2.8 2.95 98.2 0.493 24625.0 2.7 4.1 --

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 2.8 94.11 -- -- 39433 39433 2102 96.63 -- 0.22949 0.22723 0.27237 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 2.8 2.873 -- 146 2945 0.335 0.356 -- 98.03
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.901
Anisotropic B[1][1] -0.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.12
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.637
r_scbond_it 1.428
r_mcangle_it 1.107
r_mcbond_other 0.089
r_mcbond_it 0.575
r_gen_planes_other 0.002
r_gen_planes_refined 0.005
r_chiral_restr 0.068
r_dihedral_angle_4_deg 17.898
r_dihedral_angle_3_deg 18.773
r_dihedral_angle_2_deg 36.373
r_dihedral_angle_1_deg 6.54
r_angle_other_deg 0.942
r_angle_refined_deg 1.345
r_bond_other_d 0.002
r_bond_refined_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11626
Nucleic Acid Atoms 0
Heterogen Atoms 216
Solvent Atoms 116

Software

Computing
Computing Package Purpose
MxCube Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
PHASER model building
MxCube data collection