X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 291.0
Details 100 mM MES/NaOH, 30 % MPD, 10 mM Peptide DSYTC, 3 mM DTT, 120 mM Glycine, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 223.55 α = 90
b = 223.55 β = 90
c = 223.55 γ = 90
Symmetry
Space Group I 21 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2000-03-12
Diffraction Radiation
Monochromator Protocol
double crystal monochromator, Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.0499 MPG/DESY, HAMBURG BW6

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
2.57 20 93.2 0.068 6.8 -- 2.7 151692 151692 -- -- 47.1
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)
2.57 2.68 59.4 0.349 -- 2.0 2.1 5205

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 2.57 19.92 -- 0.0 56352 56352 2881 95.8 -- -- 0.209 0.226 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 2.57 2.66 -- 189 3761 0.311 0.328 0.024 67.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 50.0
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
o_mcbond_it 1.22
o_angle_deg 1.3
o_dihedral_angle_d 22.9
o_scangle_it 3.12
o_mcangle_it 2.06
o_bond_d 0.008
o_improper_angle_d 0.9
o_scbond_it 2.06
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.33
Luzzati Sigma A (Observed) 0.3
Luzzati Resolution Cutoff (Low) 25.0
Luzzati ESD (R-Free Set) 0.37
Luzzati Sigma A (R-Free Set) 0.33
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5764
Nucleic Acid Atoms 0
Heterogen Atoms 140
Solvent Atoms 136

Software

Software
Software Name Purpose
AMoRE phasing
CNS refinement version: 1.0
MOSFLM data reduction
CCP4 data scaling version: (SCALA)