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 Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 bent cylindrical Si-mirror (Rh coating) Si(111) double-crystal monochromato 2000-03-10
CCD ADSC QUANTUM 4 bent conical Si-mirror (Rh coating) bend cylindrical Ge(111) monochromator 2000-08-20
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_scangle_it 2.89
c_scbond_it 2.06
c_mcangle_it 2.3
c_mcbond_it 1.5
c_improper_angle_d 0.84
c_dihedral_angle_d 21.8
c_angle_deg 1.3
c_bond_d 0.007
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHARP Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
SHARP model building
SCALEPACK data reduction
DENZO data collection