X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details PEG 4000, Hepes, Sodium Acetate, NADP+, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 101.44 α = 90
b = 115.16 β = 90
c = 118.55 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 4 mirrors 1999-11-21
Diffraction Radiation
Monochromator Protocol
bent conical Si-mirror (Rh coating) + bent cylindrical Ge(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 1.0000 APS 14-BM-C

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
1.8 30 93.3 0.047 0.047 -- 11.6 129222 120472 0.0 0.0 15.6
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)
1.8 1.83 70.8 0.285 0.285 3.4 1.8 4536

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
FOURIER SYNTHESIS 1.8 29.16 0.0 0.0 128789 120162 6070 93.3 -- -- 0.208 0.234 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 1.8 1.88 11992 581 11411 0.338 0.338 0.014 74.9
X Ray Diffraction 1.88 1.98 14230 718 13512 0.292 0.292 0.011 89.3
X Ray Diffraction 1.98 2.11 14989 735 14254 0.237 0.237 0.009 93.6
X Ray Diffraction 2.11 2.27 15154 774 14380 0.226 0.225 0.008 94.7
X Ray Diffraction 2.27 2.5 15385 786 14599 0.212 0.212 0.008 96.0
X Ray Diffraction 2.5 2.86 15889 809 15080 0.204 0.204 0.007 98.6
X Ray Diffraction 2.86 3.6 16116 836 15280 0.197 0.197 0.007 99.3
X Ray Diffraction 3.6 29.16 16407 831 15576 0.173 0.173 0.006 98.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 34.95
Anisotropic B[1][1] -3.46
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.37
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 7.83
RMS Deviations
Key Refinement Restraint Deviation
x_torsion_impr_deg 3.14
x_angle_deg 1.5
x_bond_d 0.009
x_torsion_deg 22.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.21
Luzzati Sigma A (Observed) 0.3
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.25
Luzzati Sigma A (R-Free Set) 0.33
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9846
Nucleic Acid Atoms 0
Heterogen Atoms 279
Solvent Atoms 1126

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
Crystallography & NMR System version: 1.0 refinement