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Crystal structure of the catalytic core domain from PFV integrase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CXU PDB ENTRY 1cxu
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 1.0 M ammonium formate, 0.2 M magnesium cloride, 5 mM dithiotreitol, 0.1 M 2-(N-morpholino)ethanesulfonic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.08 40.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.14 α = 90 b = 52.14 β = 90 c = 239.78 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2008-01-26 M SINGLE WAVELENGTH 2 1 x-ray CCD MARMOSAIC 225 mm CCD 2008-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95373 ESRF BM14 2 SYNCHROTRON ESRF BEAMLINE BM14 0.97837 ESRF BM14
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 2.2 45.18 99.5 0.105 17.4 8.9 10584 10584 32.6
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) 2.2 2.32 99.3 0.681 3.4 9.3 1477
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 SAD THROUGHOUT PDB ENTRY 1cxu 2.2 45.18 9540 1042 99.2 0.21394 0.20905 0.2391 0.25922 0.2902 RANDOM 32.046
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] 0.82 0.41 0.82 -1.23
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_2_deg 35.371 f_dihedral_angle_4_deg 16.931 f_dihedral_angle_3_deg 16.041 f_dihedral_angle_1_deg 5.838 f_scangle_it 2.472 f_scbond_it 1.746 f_angle_refined_deg 1.122 f_mcangle_it 1.025 f_mcbond_it 0.558 f_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_2_deg 35.371 f_dihedral_angle_4_deg 16.931 f_dihedral_angle_3_deg 16.041 f_dihedral_angle_1_deg 5.838 f_scangle_it 2.472 f_scbond_it 1.746 f_angle_refined_deg 1.122 f_mcangle_it 1.025 f_mcbond_it 0.558 f_nbtor_refined 0.307 f_nbd_refined 0.197 f_symmetry_vdw_refined 0.149 f_symmetry_hbond_refined 0.131 f_xyhbond_nbd_refined 0.114 f_metal_ion_refined 0.099 f_chiral_restr 0.073 f_bond_refined_d 0.01 f_gen_planes_refined 0.004 f_bond_other_d f_angle_other_deg f_gen_planes_other f_nbd_other f_nbtor_other f_xyhbond_nbd_other f_metal_ion_other f_symmetry_vdw_other f_symmetry_hbond_other f_symmetry_metal_ion_refined f_symmetry_metal_ion_other f_mcbond_other f_rigid_bond_restr f_sphericity_free f_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1241 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALA data scaling SHARP phasing REFMAC refinement