3KKR

Crystal structure of catalytic core domain of BIV integrase in crystal form I


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details ammonium sulfate, sodium nitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.32 α = 90
b = 82.32 β = 90
c = 51.06 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 200
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS HTC -- 2008-04-01
Diffraction Radiation
Monochromator Protocol
Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 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
2.45 50 99.8 -- 0.046 -- 13.4 6840 6827 2.0 2.0 39.63
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)
2.45 2.54 100.0 -- 0.225 14.6 14.0 665

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 2.453 20.978 -- 0.11 -- 6749 327 99.25 -- 0.1938 0.1916 0.242 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 2.4527 2.54 -- 178 3106 0.1996 0.2784 -- 99.0
X Ray Diffraction 3.0885 20.979 -- 149 3316 0.1885 0.2241 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.078
Anisotropic B[1][1] 1.197
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.197
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.394
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.057
f_angle_d 0.886
f_dihedral_angle_d 17.701
f_bond_d 0.006
f_plane_restr 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1191
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 122

Software

Software
Software Name Purpose
HKL-2000 data collection
PHASER phasing
PHENIX refinement version: (phenix.refine)
HKL-2000 data reduction
HKL-2000 data scaling