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_deg 22.8
x_angle_deg 1.5
x_bond_d 0.009
x_torsion_impr_deg 3.14
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

Software
Software Name Purpose
CNS refinement version: 1.0
DENZO data reduction
SCALEPACK data scaling
CNS phasing