X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 278.0
Details 100 mM ADA, pH 6, 50% SATURATED AMMONIUM SULFATE, 5% PEG200, 5 mM DTT RESERVOIR MIXED IN EQUAL VOLUME WITH THE PROTEIN AT 10 mg/mL, VAPOR DIFFUSION, HANGING DROP, temperature 278K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.89 α = 90
b = 67.66 β = 90
c = 67.17 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2004-04-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X8C 1.0000 NSLS X8C

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
1.91 50 95.3 0.039 -- -- 3.8 -- 7488 0.0 -- 10.1
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)
1.91 1.98 85.9 0.064 -- 29.8 2.9 --

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 1.91 24.63 -- 0.0 7488 7488 384 95.6 -- 0.196 0.194 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 1.91 2.0 785 48 -- 0.17 0.238 -- --
X Ray Diffraction 2.0 2.1 901 54 -- 0.192 0.243 -- --
X Ray Diffraction 2.1 2.23 904 42 -- 0.206 0.293 -- --
X Ray Diffraction 2.23 2.41 894 48 -- 0.196 0.226 -- --
X Ray Diffraction 2.41 2.65 910 48 -- 0.189 0.233 -- --
X Ray Diffraction 2.65 3.03 900 46 -- 0.206 0.293 -- --
X Ray Diffraction 3.03 3.82 906 48 -- 0.187 0.224 -- --
X Ray Diffraction 3.82 50.0 904 50 985 0.196 0.214 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 14.6
Anisotropic B[1][1] -0.59
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.98
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.2
c_scbond_it 2.24
c_mcangle_it 2.16
c_mcbond_it 1.4
c_improper_angle_d 1.13
c_dihedral_angle_d 20.9
c_angle_deg 1.1
c_bond_d 0.004
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.05
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.26
Luzzati Sigma A (R-Free Set) 0.13
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 698
Nucleic Acid Atoms 0
Heterogen Atoms 45
Solvent Atoms 128

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
MOLREP Structure Solution
CNX 2005 Structure Refinement
Software
Software Name Purpose
CNX version: 2005 refinement
MOLREP model building
HKL-2000 data collection