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 = 101.63 α = 90
b = 116.06 β = 90
c = 118.75 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
IMAGE PLATE RIGAKU RAXIS IIC Mirrors 2000-08-10
Diffraction Radiation
Monochromator Protocol
Osmic blue confocal mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 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
2.7 30 80.0 0.081 0.081 -- 11.7 38773 30991 0.0 0.0 31.9
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)
2.7 2.75 57.7 0.227 0.227 2.4 1.4 1099

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 2.7 30.0 0.0 0.0 38909 30972 1535 79.6 -- -- 0.188 0.27 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 2.71 2.83 2819 143 2676 0.304 0.298 0.025 58.7
X Ray Diffraction 2.83 2.98 3190 174 3016 0.274 0.271 0.021 66.5
X Ray Diffraction 2.98 3.17 3447 184 3263 0.264 0.261 0.019 71.9
X Ray Diffraction 3.17 3.41 3875 216 3659 0.21 0.212 0.014 79.7
X Ray Diffraction 3.41 3.75 4146 179 3967 0.201 0.21 0.016 86.1
X Ray Diffraction 3.75 4.29 4347 204 4143 0.166 0.17 0.012 89.2
X Ray Diffraction 4.29 5.4 4496 216 4280 0.139 0.136 0.009 91.6
X Ray Diffraction 5.4 29.8 4652 219 4433 0.16 0.161 0.011 91.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 44.36
Anisotropic B[1][1] -3.5
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -6.73
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 10.23
RMS Deviations
Key Refinement Restraint Deviation
x_torsion_impr_deg 2.74
x_torsion_deg 22.4
x_angle_deg 1.5
x_bond_d 0.012
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Luzzati Sigma A (Observed) 0.46
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.43
Luzzati Sigma A (R-Free Set) 0.6
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9791
Nucleic Acid Atoms 0
Heterogen Atoms 264
Solvent Atoms 210

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