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Crystal structure of recombination mediator protein RecR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VDD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 295 0.2 M Potassium chloride, 0.05 M HEPES pH 7.5, 35% v/v Pentaerythritol propoxylate (5/4 PO/OH)
Crystal Properties Matthews coefficient Solvent content 2.89 57.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.92 α = 90 b = 100.22 β = 90 c = 136.02 γ = 90
Symmetry Space Group I 2 2 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 CCD MARMOSAIC 325 mm CCD 2016-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 1.5417
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 80.68 96.8 14.6 10.3 8602
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6
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 1VDD 2.5 80.68 8176 426 96.37 0.2384 0.2361 0.2378 0.2828 0.2793 RANDOM 76.335
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] -4.04 -0.54 4.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.63 r_dihedral_angle_3_deg 16.487 r_dihedral_angle_4_deg 16.01 r_dihedral_angle_1_deg 5.754 r_mcangle_it 4.271 r_angle_other_deg 3.763 r_mcbond_it 2.616 r_mcbond_other 2.616 r_angle_refined_deg 1.114 r_chiral_restr 0.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.63 r_dihedral_angle_3_deg 16.487 r_dihedral_angle_4_deg 16.01 r_dihedral_angle_1_deg 5.754 r_mcangle_it 4.271 r_angle_other_deg 3.763 r_mcbond_it 2.616 r_mcbond_other 2.616 r_angle_refined_deg 1.114 r_chiral_restr 0.056 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_gen_planes_other 0.002 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1444 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction Aimless data scaling PHASER phasing