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Crystal structure of Porphyromonas gingivalis phosphotransacetylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AF4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% (w/v) polyethylene glycol (PEG) 3350 and 0.2 M ammonium tartrate dibasic
Crystal Properties Matthews coefficient Solvent content 2.14 42.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.355 α = 90 b = 69.066 β = 90 c = 201.947 γ = 90
Symmetry Space Group P 21 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 95 CCD ADSC QUANTUM 270 2018-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 1.7 67.32 97.2 0.065 23.28 12.3 67506
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 1.7 1.73 76.4 0.126 5.7 5.5
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 2AF4 1.7 65.44 63958 3462 97.03 0.21081 0.20902 0.218 0.24435 0.2515 RANDOM 16.051
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] 0.87 -0.93 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.688 r_dihedral_angle_4_deg 13.967 r_dihedral_angle_3_deg 12.657 r_dihedral_angle_1_deg 6.184 r_long_range_B_refined 3.284 r_long_range_B_other 2.999 r_scangle_other 1.585 r_mcangle_it 1.205 r_mcangle_other 1.204 r_angle_refined_deg 1.035
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.688 r_dihedral_angle_4_deg 13.967 r_dihedral_angle_3_deg 12.657 r_dihedral_angle_1_deg 6.184 r_long_range_B_refined 3.284 r_long_range_B_other 2.999 r_scangle_other 1.585 r_mcangle_it 1.205 r_mcangle_other 1.204 r_angle_refined_deg 1.035 r_scbond_other 0.98 r_scbond_it 0.979 r_angle_other_deg 0.859 r_mcbond_it 0.73 r_mcbond_other 0.728 r_chiral_restr 0.053 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 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 5048 Nucleic Acid Atoms Solvent Atoms 638 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction SCALA data scaling MOLREP phasing