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Crystal structure of the Rous Associated Virus Integrase catalytic domain in MES buffer pH 6.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VSD PDB entry 1VSD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 290 10 mM ZnCl2, 20% (w/v) PEG 6000, 100 mM MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.6 52.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.5 α = 90 b = 107.5 β = 90 c = 50.92 γ = 120
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 ADSC QUANTUM 315r Synchrotron optics 2009-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.281060 ESRF ID29
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 1.8 20 98.99 0.085 11.61 5.25 31174 30860
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 1.8 1.95 100 0.445 3.44 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 entry 1VSD 1.8 19.68 29451 29451 1550 100 0.19074 0.18888 0.1872 0.22632 0.2223 RANDOM 31.909
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] -0.56 -0.28 -0.56 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.727 r_dihedral_angle_4_deg 22.475 r_dihedral_angle_3_deg 15.467 r_scangle_it 6.481 r_dihedral_angle_1_deg 6.019 r_scbond_it 4.095 r_mcangle_it 2.714 r_angle_refined_deg 2.118 r_mcbond_it 1.616 r_chiral_restr 0.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.727 r_dihedral_angle_4_deg 22.475 r_dihedral_angle_3_deg 15.467 r_scangle_it 6.481 r_dihedral_angle_1_deg 6.019 r_scbond_it 4.095 r_mcangle_it 2.714 r_angle_refined_deg 2.118 r_mcbond_it 1.616 r_chiral_restr 0.183 r_bond_refined_d 0.029 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2098 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 15
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement XDS data reduction XSCALE data scaling