X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.7
Temperature 291.0
Details PEG 8000, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.29 α = 90
b = 130.56 β = 90
c = 150.47 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2000-02-15
CCD ADSC QUANTUM 4 -- 2000-02-15
Diffraction Radiation
Monochromator Protocol
-- MAD
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9763, 0.9793, 0.9393 ESRF ID14-4
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9786, 0.9793, 0.9393 ESRF ID14-4

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 20 98.2 -- 0.04 -- 3.5 32005 32005 0.0 0.0 37.4
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)
3.0 3.16 98.1 -- 0.083 0.084 3.6 4597

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
MAD 3.0 19.96 -- 0.0 31603 31603 1570 97.9 -- -- 0.26 0.293 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 3.0 3.19 -- 225 4878 0.349 0.42 0.028 95.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 57.3
Anisotropic B[1][1] -15.91
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -25.74
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 41.65
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.009
c_angle_deg 1.2
c_improper_angle_d 0.79
c_scbond_it 1.63
c_dihedral_angle_d 22.3
c_mcbond_it 1.08
c_mcangle_it 1.92
c_scangle_it 2.63
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.43
Luzzati Sigma A (Observed) 0.52
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.52
Luzzati Sigma A (R-Free Set) 0.59
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8907
Nucleic Acid Atoms 0
Heterogen Atoms 8
Solvent Atoms 58

Software

Software
Software Name Purpose
SnB phasing
SHARP phasing
CNS refinement version: 1.1
DENZO data reduction
SCALEPACK data scaling
SHAKE-N-BAKE phasing