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Crystal structure of Porphyromonas gingivalis acetate kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IIR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M lithium sulfate monohydrate, 0.1 M Tris/HCl (pH 8.5), and 24% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.39 48.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.77 α = 90 b = 98.472 β = 91.64 c = 102.769 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS PILATUS 2M-F 2017-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
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 1.94 53.4 99.3 0.093 11.9 6.5 120952
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 1.94 1.97 92.2 0.24 5.78 6.5
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 2IIR 1.94 53.4 114747 6081 99.18 0.1907 0.18919 0.1981 0.21942 0.2246 RANDOM 18.041
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] -0.53 -0.62 -0.53 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.762 r_dihedral_angle_4_deg 18.452 r_dihedral_angle_3_deg 13.833 r_dihedral_angle_1_deg 6.424 r_long_range_B_refined 5.332 r_long_range_B_other 5.225 r_scangle_other 3.964 r_mcangle_it 2.525 r_mcangle_other 2.525 r_scbond_it 2.516
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.762 r_dihedral_angle_4_deg 18.452 r_dihedral_angle_3_deg 13.833 r_dihedral_angle_1_deg 6.424 r_long_range_B_refined 5.332 r_long_range_B_other 5.225 r_scangle_other 3.964 r_mcangle_it 2.525 r_mcangle_other 2.525 r_scbond_it 2.516 r_scbond_other 2.515 r_mcbond_it 1.619 r_mcbond_other 1.618 r_angle_refined_deg 1.37 r_angle_other_deg 0.948 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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 12114 Nucleic Acid Atoms Solvent Atoms 974 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement DIALS data reduction SCALA data scaling MOLREP phasing