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Human foamy virus integrase - catalytic core. Magnesium-bound structure.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X74 PDB ENTRY 2X74
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 1.8-2M AMMONIUM FORMATE, 100MM HEPES, PH 7.5 5MM MGCL2, 10-15% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.64 40.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.35 α = 90 b = 89.19 β = 90 c = 177.23 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 180 CCD ADSC QUANTUM 315r TOROIDAL FOCUSING MIRROR 2008-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.29 44.59 97.4 0.07 15.9 4.5 59482
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.41 89.3 0.54 2 2.9
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 ENTRY 2X74 2.29 44.6 56404 3009 97.23 0.22757 0.22485 0.2182 0.27807 0.2672 RANDOM 48.333
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] 3.3 -2.86 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.209 r_dihedral_angle_4_deg 19.375 r_dihedral_angle_3_deg 18.891 r_dihedral_angle_1_deg 5.467 r_scangle_it 2.828 r_mcangle_it 1.953 r_scbond_it 1.813 r_angle_refined_deg 1.192 r_mcbond_it 1.083 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.209 r_dihedral_angle_4_deg 19.375 r_dihedral_angle_3_deg 18.891 r_dihedral_angle_1_deg 5.467 r_scangle_it 2.828 r_mcangle_it 1.953 r_scbond_it 1.813 r_angle_refined_deg 1.192 r_mcbond_it 1.083 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8689 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing