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Crystal structure of Porphyromonas gingivalis phosphotransacetylase in complex with acetyl-CoA
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 2.26 45.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.693 α = 90 b = 130.023 β = 90 c = 52.602 γ = 90
Symmetry Space Group P 21 21 2
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 2018-05-28 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 2.04 43.45 100 0.092 16.93 12.6 42700
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 2.04 2.07 99.1 0.227 5.5 11.4
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 2.04 43.45 40529 2120 99.93 0.19868 0.1966 0.2055 0.23769 0.2458 RANDOM 21.547
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] 0.25 0.65 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.854 r_dihedral_angle_4_deg 15.609 r_dihedral_angle_3_deg 15.179 r_dihedral_angle_1_deg 6.652 r_long_range_B_refined 5.444 r_long_range_B_other 5.438 r_scangle_other 4.282 r_scbond_it 2.739 r_scbond_other 2.739 r_mcangle_it 2.588
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.854 r_dihedral_angle_4_deg 15.609 r_dihedral_angle_3_deg 15.179 r_dihedral_angle_1_deg 6.652 r_long_range_B_refined 5.444 r_long_range_B_other 5.438 r_scangle_other 4.282 r_scbond_it 2.739 r_scbond_other 2.739 r_mcangle_it 2.588 r_mcangle_other 2.588 r_mcbond_it 1.707 r_mcbond_other 1.703 r_angle_refined_deg 1.523 r_angle_other_deg 0.956 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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 5025 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement DIALS data reduction SCALA data scaling MOLREP phasing