X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 298.0
Details PEG3500, MPD, ETHYLENE GLYCOL, MJ33, CALCIUM CHLORIDE, HEPES BUFFER, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 139.06 α = 90
b = 145.1 β = 90
c = 28.09 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV MIRRORS 2001-08-27
Diffraction Radiation
Monochromator Protocol
OSMIC MIRRORS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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 24.5 95.8 0.081 -- -- 4.3 19931 19092 0.0 -3.0 18.7
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 78.0 -- -- 2.3 3.2 1489

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 2.09 24.51 -- 3.0 17540 14657 711 83.6 0.228 0.214 0.211 0.252 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 2.09 2.22 1768 88 1680 0.236 0.267 0.029 61.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 38.5
Anisotropic B[1][1] 4.87
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.72
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.15
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.4
c_scbond_it 1.6
c_mcangle_it 1.62
c_mcbond_it 0.98
c_improper_angle_d 0.83
c_bond_d 0.005
c_angle_deg 1.1
c_dihedral_angle_d 22.2
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.25
Luzzati Sigma A (Observed) 0.19
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.31
Luzzati Sigma A (R-Free Set) 0.26
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1890
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 210

Software

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