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Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DLR PDB ENTRIES 3DLR; 1EX4 CHAIN A RESIDUES 223-266; 7bp B-DNA experimental model PDB 1EX4 PDB ENTRIES 3DLR; 1EX4 CHAIN A RESIDUES 223-266; 7bp B-DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 1.35M ammonium sulfate, 25% (v/v) glycerol, 4.8% (v/v) 1,6-hexanediol, 50mM Mes-NaOH, pH 6.5, vapor diffusion, hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.9 68.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.48 α = 90 b = 158.48 β = 90 c = 124.19 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 100 AREA DETECTOR ADSC 2009-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9796 Diamond I02
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 2.88 38.999 99.2 0.12 6.3 35972 35972 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.88 3.04 100
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 ENTRIES 3DLR; 1EX4 CHAIN A RESIDUES 223-266; 7bp B-DNA 2.88 38.999 34156 1777 98.96 0.20305 0.20202 0.2059 0.22232 0.2225 RANDOM 74.31
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] 1.56 1.56 -3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.294 r_dihedral_angle_4_deg 19.042 r_dihedral_angle_3_deg 18.24 r_dihedral_angle_1_deg 6.434 r_scangle_it 2.701 r_angle_refined_deg 1.657 r_scbond_it 1.591 r_mcangle_it 1.062 r_mcbond_it 0.538 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.294 r_dihedral_angle_4_deg 19.042 r_dihedral_angle_3_deg 18.24 r_dihedral_angle_1_deg 6.434 r_scangle_it 2.701 r_angle_refined_deg 1.657 r_scbond_it 1.591 r_mcangle_it 1.062 r_mcbond_it 0.538 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 4150 Nucleic Acid Atoms 732 Solvent Atoms 12 Heterogen Atoms 34
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection