X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 283.0
Details PEG-8000, calcium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.4 α = 90
b = 66.7 β = 90
c = 117.1 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 1999-12-08
Diffraction Radiation
Monochromator Protocol
Standard SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE 0.934 ESRF --

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 20 95.1 0.059 -- -- 5.8 -- 21058 -- -3.0 8.7
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)
2.0 2.03 95.8 0.185 -- -- -- 1039

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
FOURIER SYNTHESIS 2.0 20.0 -- 0.0 21040 20468 990 92.5 -- -- 0.168 0.203 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 2.0 2.04 1006 50 956 0.184 0.23 0.033 88.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 16.8
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.47
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.48
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 1.99
c_angle_deg 1.2
c_dihedral_angle_d 21.0
c_scangle_it 2.76
c_bond_d 0.005
c_mcangle_it 1.68
c_improper_angle_d 1.14
c_mcbond_it 1.17
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Luzzati Sigma A (Observed) 0.1
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.23
Luzzati Sigma A (R-Free Set) 0.13
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2363
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 295

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PDB model building version: entry 6atj without water was used as a starting model
CNS refinement version: 1.1
PDB phasing version: ENTRY 6ATJ WITHOUT WATER WAS USED AS A STARTING MODEL