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_angle_deg 1.5
x_bond_d 0.012
x_torsion_impr_deg 2.74
x_torsion_deg 22.4
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 9793
Nucleic Acid Atoms 0
Heterogen Atoms 264
Solvent Atoms 210

Software

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