X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details sodium citrate and imidizole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75.86 α = 90
b = 75.86 β = 90
c = 253.81 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV MSC Blue mirrors 2003-07-10
Diffraction Radiation
Monochromator Protocol
mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 1.54 -- --

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
2.5 50 96.0 -- 0.119 -- 5.5 25505 25505 0.0 -3.0 44.7
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)
2.5 2.59 86.8 -- 0.377 3.5 4.0 2245

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 2.5 48.67 -- 0.02 25884 24693 1191 93.0 0.222 0.221 0.221 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 2.5 2.66 -- 150 3235 0.316 0.325 0.027 78.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 47.8
Anisotropic B[1][1] -2.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.0
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 1.69
c_bond_d 0.008
c_angle_deg 1.3
c_dihedral_angle_d 21.8
c_improper_angle_d 0.92
c_mcbond_it 1.21
c_mcangle_it 1.99
c_scangle_it 2.54
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.35
Luzzati Sigma A (Observed) 0.4
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.42
Luzzati Sigma A (R-Free Set) 0.44
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2325
Nucleic Acid Atoms 0
Heterogen Atoms 49
Solvent Atoms 63

Software

Software
Software Name Purpose
CNS refinement version: 1.0
SCALEPACK data scaling
CNS phasing