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_angle_deg 1.4
c_scangle_it 6.45
c_improper_angle_d 0.84
c_scbond_it 7.45
c_mcangle_it 1.52
c_bond_d 0.007
c_dihedral_angle_d 23.5
c_mcbond_it 0.94
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

Software
Software Name Purpose
BIOTEX data collection
SCALEPACK data scaling
CNS refinement
BIOTEX data reduction
CNS phasing