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Crystal structure of RecR from Pseudomonas aeruginosa PAO1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VDP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 1.26M sodium phosphate mono basic monohydrate, 0.14M potassium phosphate dibasic, 10% PEG 6000, 100mM HEPES/sodium hydroxide pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.94 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.075 α = 90 b = 70.075 β = 90 c = 369.022 γ = 120
Symmetry Space Group P 61 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 PIXEL DECTRIS PILATUS3 6M 2016-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97776 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 2.2 50 99.7 0.034 0.999 20.3 20 27394
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 97.9 0.215 0.949 3.3 15
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 3vdp 2.2 50 25500 1895 94.5 0.18 0.178 0.1854 0.213 0.2178 RANDOM 30.52
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] 0.07 0.04 0.07 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.555 r_dihedral_angle_4_deg 16.404 r_dihedral_angle_3_deg 13.533 r_long_range_B_other 9.184 r_long_range_B_refined 9.182 r_scangle_other 7.503 r_dihedral_angle_1_deg 5.486 r_scbond_it 5.384 r_scbond_other 5.382 r_mcangle_other 3.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.555 r_dihedral_angle_4_deg 16.404 r_dihedral_angle_3_deg 13.533 r_long_range_B_other 9.184 r_long_range_B_refined 9.182 r_scangle_other 7.503 r_dihedral_angle_1_deg 5.486 r_scbond_it 5.384 r_scbond_other 5.382 r_mcangle_other 3.79 r_mcangle_it 3.786 r_mcbond_it 2.59 r_mcbond_other 2.581 r_angle_refined_deg 1.584 r_angle_other_deg 1.082 r_chiral_restr 0.119 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2938 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing