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_scangle_it 3.71
x_scbond_it 2.46
x_mcangle_it 2.27
x_mcbond_it 1.47
x_torsion_impr_deg 1.07
x_torsion_deg 24.3
x_angle_deg 1.8
x_bond_d 0.017
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

Computing
Computing Package Purpose
MAR Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
SHARP Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
SHARP model building