X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8
Temperature 298.0
Details PEG4000, Tris/HCl. 300mM NaCl, glycerol, 10mM CaCl2, pH 8.0, VAPOR DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.08 α = 90
b = 54.78 β = 90.3
c = 89.15 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS II Osmic Confocal optics --
Diffraction Radiation
Monochromator Protocol
Osmic Confocal optics SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 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
2.1 99 99.4 0.119 -- -- 3.0 37716 37503 -- -3.0 26.4
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)
2.1 2.14 99.0 0.688 -- 1.8 2.7 1860

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 2.1 30.38 -- 2.0 -- 35649 3560 97.8 -- 0.222 0.222 0.262 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 2.1 2.23 -- 583 5257 0.281 0.319 0.013 97.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 31.7
Anisotropic B[1][1] -7.5
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.38
Anisotropic B[2][2] 8.31
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.81
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 6.45
c_scbond_it 7.45
c_mcangle_it 1.52
c_mcbond_it 0.94
c_improper_angle_d 0.84
c_bond_d 0.007
c_angle_deg 1.4
c_dihedral_angle_d 23.5
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.27
Luzzati Sigma A (Observed) 0.27
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.32
Luzzati Sigma A (R-Free Set) 0.31
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4743
Nucleic Acid Atoms 0
Heterogen Atoms 56
Solvent Atoms 258

Software

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