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Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with manganese at 2.55 resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L2R PDB entry 3L2R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 1.35 M ammonium sulfate, 25% (v/v) glycerol, 4.8% (v/v) 1,6-hexanediol, 50 mM Mes-NaOH, 1mM EDTA, pH 6.5, vapor diffusion, hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.97 69.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.09 α = 90 b = 160.09 β = 90 c = 123.94 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 2010-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97950 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 2.55 39.206 98.9 0.084 14.1 5.5 52142 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.55 2.69 99 0.931 0.931 2 5.4 7536
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3L2R 2.55 39.21 52062 2627 98.33 0.2 0.1986 0.1973 0.2217 0.2113 RANDOM 58.3457
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] 1.46 1.46 -2.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.983 r_dihedral_angle_4_deg 18.176 r_dihedral_angle_3_deg 15.897 r_dihedral_angle_1_deg 6.015 r_scangle_it 2.99 r_scbond_it 1.777 r_angle_refined_deg 1.496 r_mcangle_it 1.391 r_mcbond_it 0.725 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.983 r_dihedral_angle_4_deg 18.176 r_dihedral_angle_3_deg 15.897 r_dihedral_angle_1_deg 6.015 r_scangle_it 2.99 r_scbond_it 1.777 r_angle_refined_deg 1.496 r_mcangle_it 1.391 r_mcbond_it 0.725 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4339 Nucleic Acid Atoms 732 Solvent Atoms 274 Heterogen Atoms 39
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection PHASER phasing