X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 298.0
Details NaCl, citrate/phosphate buffer, PEG 3400, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 71.4 α = 90
b = 111.4 β = 97.7
c = 71.9 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV yale mirrors 1994-04-23
Diffraction Radiation
Monochromator Protocol
mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 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
2.5 60 84.6 0.101 0.101 -- 3.0 -- 32692 0.0 0.0 21.9
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 2.66 56.0 0.265 0.265 1.5 2.0 4008

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 60.03 0.0 0.0 -- 32692 3240 84.6 -- -- 0.232 0.288 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 -- 413 3760 0.372 0.409 0.02 64.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 58.1
Anisotropic B[1][1] 0.91
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 2.09
Anisotropic B[2][2] -12.97
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 12.06
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.7
c_improper_angle_d 1.01
c_bond_d 0.01
c_dihedral_angle_d 23.9
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.37
Luzzati Sigma A (Observed) 0.61
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.48
Luzzati Sigma A (R-Free Set) 0.67
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7068
Nucleic Acid Atoms 0
Heterogen Atoms 100
Solvent Atoms 118

Software

Software
Software Name Purpose
MERLOT phasing
CNS refinement version: 1.0
BIOTEX data reduction
BIOTEX data scaling