X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 295.5
Details 30% PEG 4000, 0.2 M ammonium sulfate, and 0.1 M sodium acetate at pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.37 α = 90
b = 61.69 β = 107.49
c = 71.14 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 173
2 173
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE -- -- 1999-02-13
IMAGE PLATE -- -- 1999-06-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 -- SSRL BL7-1
SYNCHROTRON SSRL BEAMLINE BL7-1 -- SSRL BL7-1
SYNCHROTRON SSRL BEAMLINE BL9-2 -- SSRL BL9-2
SYNCHROTRON SSRL BEAMLINE BL9-2 -- SSRL BL9-2

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
1.7 48 98.8 0.05 -- -- 8.0 48000 48000 0.0 0.0 15.4
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)
1.7 1.76 88.8 0.26 -- -- 3.0 4269

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
-- 1.7 48.27 -- 0.0 48516 46658 1858 96.0 0.22 0.22 0.22 0.24 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 1.7 1.81 -- 244 6724 0.251 0.276 0.018 86.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 21.4
Anisotropic B[1][1] 3.7
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.54
Anisotropic B[2][2] -2.51
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.19
RMS Deviations
Key Refinement Restraint Deviation
c_mcangle_it 1.66
c_improper_angle_d 3.1
c_scangle_it 1.68
c_scbond_it 1.1
c_angle_deg 1.5
c_mcbond_it 0.94
c_bond_d 0.007
c_dihedral_angle_d 23.6
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.21
Luzzati Sigma A (Observed) 0.13
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.24
Luzzati Sigma A (R-Free Set) 0.17
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2810
Nucleic Acid Atoms 0
Heterogen Atoms 83
Solvent Atoms 297

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASES Structure Solution
CNS 0.9 Structure Refinement
Software
Software Name Purpose
PHASES model building
CNS version: 0.9 refinement