X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 293.0
Details PEG 4000, tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.91 α = 90
b = 108.78 β = 90.19
c = 56.08 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
CCD MAR CCD 130 mm -- 2004-04-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID13 0.954 ESRF ID13

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
2.25 30.45 99.0 0.059 0.059 -- 3.4 31524 31524 0.0 0.0 --
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)
2.25 2.37 97.4 0.222 0.222 4.1 2.8 4483

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
isomorphous to native crystals 2.25 30.45 -- 0.0 -- 31496 1586 98.9 -- -- 0.202 0.239 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 2.25 2.33 3107 156 -- 0.2489 0.311 -- 97.0
X Ray Diffraction 2.33 2.42 3020 153 -- 0.2319 0.3005 -- 97.0
X Ray Diffraction 2.42 2.53 3114 149 -- 0.2244 0.2742 -- 97.0
X Ray Diffraction 2.53 2.67 3156 157 -- 0.2293 0.2873 -- 99.0
X Ray Diffraction 2.67 2.83 3136 144 -- 0.2213 0.2762 -- 99.5
X Ray Diffraction 2.83 3.05 3191 166 -- 0.2044 0.2508 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 26.46
Anisotropic B[1][1] -3.902
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.701
Anisotropic B[2][2] -1.997
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.899
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.408
c_mcangle_it 2.125
c_scbond_it 2.239
c_mcbond_it 1.32
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.26
Luzzati Sigma A (Observed) 0.23
Luzzati ESD (R-Free Set) 0.31
Luzzati Sigma A (R-Free Set) 0.31
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3336
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 182

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
CNS Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.005 data extraction
CNS refinement
CNS density modification
SCALA version: CCP4_3.1.4 data processing
Mosflm version: Version 6.2.3 reflection data processing