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Crystal structure of catalytic core domain of BIV integrase in crystal form II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KKR PDB ID 3KKR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 PEG 10000, sodium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.054 α = 90 b = 88.054 β = 90 c = 81.775 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 IMAGE PLATE RIGAKU RAXIS HTC 2009-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1 2.2 50 99.8 0.103 26.5 12.7 16868 2 2 27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 99.9 0.5 6.6 13 1643
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ID 3KKR 2.2 19.48 16303 797 96.7 0.239 0.239 0.2393 0.272 0.2735 RANDOM 34
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 4.17 4.17 -8.35
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.7 c_scangle_it 3.19 c_scbond_it 2.15 c_mcangle_it 2.13 c_mcbond_it 1.33 c_angle_deg 1.3 c_improper_angle_d 0.78 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2359 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 20
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling