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The Pseudomonas aeruginosa RccR protein complexed with KDPG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IVN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 0.15 M DL-malic acid pH 7.0, 0.1 M imidazole pH 7.0, 22% polyethylene glycol monomethyl ether 550 (v/v)
Crystal Properties Matthews coefficient Solvent content 3.47 64.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.138 α = 90 b = 81.624 β = 90 c = 137.888 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 AGILENT ATLAS CCD 2020-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
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 1.9 50 75.21 0.089 25.4 11.7 26374
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 1.901 1.969 0.652
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.9 26.01 25023 1357 75.23 0.20127 0.199 0.2076 0.24252 0.2447 RANDOM 30.219
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] 0.02 -0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.114 r_long_range_B_refined 8.324 r_long_range_B_other 8.324 r_dihedral_angle_1_deg 6.68 r_scangle_other 6.211 r_dihedral_angle_2_deg 4.764 r_mcangle_it 4.561 r_mcangle_other 4.56 r_scbond_other 4.078 r_scbond_it 4.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.114 r_long_range_B_refined 8.324 r_long_range_B_other 8.324 r_dihedral_angle_1_deg 6.68 r_scangle_other 6.211 r_dihedral_angle_2_deg 4.764 r_mcangle_it 4.561 r_mcangle_other 4.56 r_scbond_other 4.078 r_scbond_it 4.07 r_mcbond_it 3.095 r_mcbond_other 3.093 r_angle_refined_deg 1.477 r_angle_other_deg 0.49 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2124 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing PDB_EXTRACT data extraction