X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 297.0
Details 2M ammonium sulfate, 5% dioxane, 100mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 190.72 α = 90
b = 65.71 β = 90
c = 77.91 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2000-03-09
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8424 EMBL/DESY, Hamburg BW7B

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
1.86 34.26 99.0 0.036 -- -- 4.6 82679 82679 0.0 -3.0 20.6
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)
1.86 1.88 93.8 0.235 0.235 4.5 3.0 2430

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
MAD 1.9 34.26 -3.0 -3.0 78040 77441 1552 99.2 -- -- 0.211 0.247 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 1.9 1.99 9538 193 9345 0.254 0.255 0.018 98.8
X Ray Diffraction 1.99 2.09 9490 193 9297 0.206 0.206 0.015 98.8
X Ray Diffraction 2.09 2.22 9622 191 9431 0.204 0.203 0.015 99.2
X Ray Diffraction 2.22 2.39 9581 192 9389 0.225 0.225 0.016 99.1
X Ray Diffraction 2.39 2.63 9659 190 9469 0.191 0.192 0.014 99.2
X Ray Diffraction 2.63 3.02 9687 195 9492 0.201 0.202 0.014 99.3
X Ray Diffraction 3.02 3.8 9736 195 9541 0.207 0.206 0.015 99.2
X Ray Diffraction 3.8 34.26 10128 203 9925 0.216 0.217 0.015 99.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 31.76
Anisotropic B[1][1] -1.36
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.89
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.53
RMS Deviations
Key Refinement Restraint Deviation
x_angle_deg 1.8
x_mcbond_it 1.47
x_scangle_it 3.71
x_torsion_deg 24.3
x_mcangle_it 2.27
x_bond_d 0.017
x_torsion_impr_deg 1.07
x_scbond_it 2.46
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.14
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.25
Luzzati Sigma A (R-Free Set) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5878
Nucleic Acid Atoms 0
Heterogen Atoms 88
Solvent Atoms 396

Software

Software
Software Name Purpose
SHARP phasing
CNS refinement version: 1.0
MAR345 data collection
XDS data scaling