X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.8
Temperature 292.0
Details PEG 6000, sodium acetate, n-octanoylsucrose, S-adenosyl-L-homocysteine, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.34 α = 90
b = 45.34 β = 90
c = 446.02 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 bent conical Si-mirror (Rh coating) bend cylindrical Ge(111) monochromator 2000-08-20
CCD ADSC QUANTUM 4 bent cylindrical Si-mirror (Rh coating) Si(111) double-crystal monochromato 2000-03-10
Diffraction Radiation
Monochromator Protocol
Si(111) double-crystal monochromator MAD
bend cylindrical Ge(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-D 0.9793, 0.9795, 0.9641 APS 14-BM-D
SYNCHROTRON APS BEAMLINE 14-BM-C 1 APS 14-BM-C

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 30 98.0 -- -- -- -- 33417 33305 3.0 3.0 19.3
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 2.07 93.4 -- -- -- -- --

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 2.0 28.21 -- 3.0 33417 32625 1619 95.7 0.235 0.222 0.222 0.27 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 2.13 -- 204 3932 0.231 0.296 0.021 71.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 33.9
Anisotropic B[1][1] 2.0
Anisotropic B[1][2] 1.83
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.01
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 2.06
c_bond_d 0.007
c_angle_deg 1.3
c_scangle_it 2.89
c_improper_angle_d 0.84
c_mcbond_it 1.5
c_dihedral_angle_d 21.8
c_mcangle_it 2.3
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.24
Luzzati Sigma A (Observed) 0.14
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.31
Luzzati Sigma A (R-Free Set) 0.24
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4331
Nucleic Acid Atoms 0
Heterogen Atoms 60
Solvent Atoms 200

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SHARP phasing
CNS refinement version: 1.0