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Crystal structure of the beta-porphyranase BpGH16B (BACPLE_01689) from the human gut bacterium Bacteroides plebeius
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JUU PDB ENTRY 3JUU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 23-25 % PEG 3350, 100 MM TRIS PH 8.5 AND 5 MM CALCIUM CHLORIDE
Crystal Properties Matthews coefficient Solvent content 2.69 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.12 α = 90 b = 107.23 β = 90 c = 137.26 γ = 90
Symmetry Space Group P 2 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 100 CCD MARMOSAIC 325 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 2.4 43.74 99.9 0.13 10.5 6.3 30374 2
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 2.4 2.5 99.7 0.44 4.2 6.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3JUU 2.4 40 28740 1534 99.72 0.20261 0.20003 0.25014 0.2327 RANDOM 19.518
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] -6.41 25.27 -18.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.23 r_dihedral_angle_4_deg 21.125 r_dihedral_angle_3_deg 17.068 r_dihedral_angle_1_deg 6.955 r_scangle_it 2.523 r_scbond_it 1.527 r_angle_refined_deg 1.294 r_mcangle_it 1.091 r_mcbond_it 0.57 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.23 r_dihedral_angle_4_deg 21.125 r_dihedral_angle_3_deg 17.068 r_dihedral_angle_1_deg 6.955 r_scangle_it 2.523 r_scbond_it 1.527 r_angle_refined_deg 1.294 r_mcangle_it 1.091 r_mcbond_it 0.57 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4788 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement MOLREP phasing