X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 3.8
Temperature 278.0
Details PEG4000, ammonium acetate, sodium acetate, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 278K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 98.8 α = 90
b = 98.8 β = 90
c = 149.34 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
DIFFRACTOMETER WEISSENBERG -- 1999-11-04
Diffraction Radiation
Monochromator Protocol
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 1.0 Photon Factory BL-18B

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
2.8 50 98.7 0.095 0.095 -- 6.1 21101 21088 0.0 0.0 17.8
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)
2.8 2.9 97.1 0.299 0.299 3.2 3.7 2041

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 2.8 49.78 -- 0.0 21088 21088 1064 98.7 0.1988 0.1988 0.196 0.251 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 2.8 2.98 -- 149 3257 0.277 0.356 0.029 97.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 32.1
Anisotropic B[1][1] 5.93
Anisotropic B[1][2] 7.15
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.93
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -11.85
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.3
c_bond_d 0.006
c_dihedral_angle_d 22.6
c_mcangle_it 4.73
c_mcbond_it 3.09
c_scangle_it 7.09
c_scbond_it 4.95
c_improper_angle_d 0.8
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.39
Luzzati Sigma A (R-Free Set) 0.53
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4319
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 115

Software

Software
Software Name Purpose
AMoRE phasing
CNS refinement version: 1.1
DENZO data reduction
SCALEPACK data scaling