X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 292.0
Details PEG 4000, lauryl-dimethylamine-N-oxide, heptane-1,2,3-triol, tricine buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.93 α = 90
b = 80.31 β = 92.41
c = 246.57 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH Flat mirror (vertical focusing) 2000-06-10
Diffraction Radiation
Monochromator Protocol
single crystal Si(311) bent monochromator (horizontal focusing) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 0.98 SSRL BL9-1

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
3.25 49.32 98.9 -- 0.119 -- 7.3 47751 47751 0.0 0.0 64.3
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)
3.25 3.43 98.7 -- 0.45 1.7 7.4 6920

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
MOLECULAR REPLACEMENT 3.25 49.32 0.0 0.0 47695 47695 2385 98.5 0.263 0.263 0.248 0.287 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 3.25 3.37 4737 226 -- 0.328 0.373 -- 98.4
X Ray Diffraction 3.37 3.5 4746 241 -- 0.291 0.31 -- 98.5
X Ray Diffraction 3.5 3.66 4697 255 -- 0.279 0.324 -- 98.5
X Ray Diffraction 3.66 3.85 4735 239 -- 0.243 0.286 -- 98.3
X Ray Diffraction 3.85 4.09 4756 228 -- 0.24 0.32 -- 98.6
X Ray Diffraction 4.09 4.41 4732 229 -- 0.218 0.247 -- 98.4
X Ray Diffraction 4.41 4.85 4790 257 -- 0.208 0.247 -- 98.5
X Ray Diffraction 4.85 5.56 4777 234 -- 0.236 0.289 -- 98.5
X Ray Diffraction 5.56 7.0 4804 240 -- 0.233 0.28 -- 98.5
X Ray Diffraction 7.0 50.0 4921 236 -- 0.262 0.28 -- 98.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 74.9
Anisotropic B[1][1] 46.477
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -11.191
Anisotropic B[2][2] -21.432
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -25.045
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.883
c_dihedral_angle_d 19.25
c_angle_d 1.28
c_bond_d 0.00773
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.42
Luzzati Sigma A (Observed) 0.56
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.5
Luzzati Sigma A (R-Free Set) 0.6
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14404
Nucleic Acid Atoms 0
Heterogen Atoms 964
Solvent Atoms 129

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
CNS Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
CNS model building