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Crystal structure of recombination mediator protein RecF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O5V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7 295 0.1M Sodium malonate pH 7.0, 0.1M HEPES pH 7.0, 0.5 % v/v Jeffamine ED-2001
Crystal Properties Matthews coefficient Solvent content 2.85 56.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.7 α = 90 b = 74.38 β = 90 c = 153.359 γ = 90
Symmetry Space Group P 2 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 100 CCD MARMOSAIC 225 mm CCD 2017-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95372 ESRF BM14
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 1.58 51.13 99.3 0.044 17.2 4.8 60237
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 1.58 1.6 0.355
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 2O5V 1.58 51.13 56631 2991 99.06 0.17256 0.17001 0.1841 0.2204 0.228 RANDOM 30.334
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] 0.35 -1.28 0.93
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.089 r_dihedral_angle_2_deg 27.113 r_sphericity_bonded 23.361 r_dihedral_angle_4_deg 18.654 r_dihedral_angle_3_deg 13.938 r_long_range_B_refined 7.802 r_long_range_B_other 7.693 r_scangle_other 7.326 r_mcangle_other 6.612 r_mcangle_it 6.611
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.089 r_dihedral_angle_2_deg 27.113 r_sphericity_bonded 23.361 r_dihedral_angle_4_deg 18.654 r_dihedral_angle_3_deg 13.938 r_long_range_B_refined 7.802 r_long_range_B_other 7.693 r_scangle_other 7.326 r_mcangle_other 6.612 r_mcangle_it 6.611 r_scbond_it 6.313 r_scbond_other 6.311 r_dihedral_angle_1_deg 6.228 r_mcbond_it 5.36 r_mcbond_other 5.356 r_rigid_bond_restr 3.227 r_angle_refined_deg 1.856 r_angle_other_deg 1.101 r_chiral_restr 0.117 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2629 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction Aimless data scaling PHASER phasing