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Crystal structure of OXA-17
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FOF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 20% PEG 3350, 0.2 M Sodium formate, 0.1 M Tris-HCl pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.84 56.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.56 α = 90 b = 102.812 β = 90 c = 126.752 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 100 PIXEL DECTRIS PILATUS 6M 2023-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.97942 PAL/PLS 11C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.98 47.64 99.29 0.157 0.157 0.174 0.073 0.991 13.99 6 44778
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.05 0.275
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 1FOF 1.98 47.64 42612 2183 99.11 0.20324 0.2005 0.2096 0.25739 0.2642 RANDOM 34.384
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]
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 16.147 r_long_range_B_other 16.003 r_dihedral_angle_3_deg 15.382 r_dihedral_angle_2_deg 6.332 r_dihedral_angle_1_deg 6.304 r_scangle_other 5.943 r_mcangle_other 4.61 r_mcangle_it 4.608 r_scbond_it 3.803 r_scbond_other 3.803
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 16.147 r_long_range_B_other 16.003 r_dihedral_angle_3_deg 15.382 r_dihedral_angle_2_deg 6.332 r_dihedral_angle_1_deg 6.304 r_scangle_other 5.943 r_mcangle_other 4.61 r_mcangle_it 4.608 r_scbond_it 3.803 r_scbond_other 3.803 r_mcbond_other 3.201 r_mcbond_it 3.2 r_angle_refined_deg 1.416 r_angle_other_deg 0.491 r_chiral_restr 0.074 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 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 3918 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling HKL-3000 phasing PDB_EXTRACT data extraction