X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.8
Temperature 278.0
Details ammonium sulphate, MPD, dioxane, hepes, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 278K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.82 α = 90
b = 160.13 β = 94.3
c = 88.96 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH null 2000-12-12
CCD MARRESEARCH null 2000-09-16
Diffraction Radiation
Monochromator Protocol
null SINGLE WAVELENGTH
null MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ELETTRA BEAMLINE 5.2R 0.99983 ELETTRA 5.2R
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.97487, 0.97845, 0.97848, 0.97864, 0.97874, 0.95583, 0.9080, 1.0022 EMBL/DESY, HAMBURG BW7A

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
1.96 50 92.6 0.042 -- -- 5.44 144731 134114 0.0 0.0 25.6
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)
1.95 1.98 73.1 0.223 -- 2.43 2.85 5367

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 1.96 27.42 -- 0.0 144731 134114 4041 92.3 0.21 0.21 0.21 0.256 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 1.96 2.08 -- 614 20020 0.309 0.371 0.015 85.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 46.9
Anisotropic B[1][1] 10.65
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 3.59
Anisotropic B[2][2] -1.35
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -9.3
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.16
c_dihedral_angle_d 25.7
c_angle_deg 1.9
c_bond_d 0.017
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.27
Luzzati Sigma A (Observed) 0.29
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.35
Luzzati Sigma A (R-Free Set) 0.37
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13805
Nucleic Acid Atoms 0
Heterogen Atoms 237
Solvent Atoms 1003

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHAKE-N-BAKE V. 2.0 Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
SnB version: v2.0 model building