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Structure of the PonA1 protein from Mycobacterium Tuberculosis in complex with penicillin V
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CRF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 0.1 M HEPES, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.17 43.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.341 α = 90 b = 60.58 β = 90 c = 133.904 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 CCD MARMOSAIC 225 mm CCD 2014-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.75 30 99.5 0.098 23.5 7.2 39656
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 1.75 1.78 99 0.634 3.1 7.1
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 5CRF 1.75 30 37678 1921 99.44 0.14895 0.14692 0.1606 0.18937 0.1975 RANDOM 20.069
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] 0.93 -0.44 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.867 r_dihedral_angle_3_deg 12.857 r_dihedral_angle_4_deg 10.775 r_long_range_B_refined 5.922 r_long_range_B_other 5.922 r_dihedral_angle_1_deg 5.553 r_scangle_other 2.087 r_angle_refined_deg 1.719 r_mcangle_it 1.526 r_mcangle_other 1.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.867 r_dihedral_angle_3_deg 12.857 r_dihedral_angle_4_deg 10.775 r_long_range_B_refined 5.922 r_long_range_B_other 5.922 r_dihedral_angle_1_deg 5.553 r_scangle_other 2.087 r_angle_refined_deg 1.719 r_mcangle_it 1.526 r_mcangle_other 1.526 r_scbond_it 1.291 r_scbond_other 1.288 r_angle_other_deg 0.99 r_mcbond_it 0.896 r_mcbond_other 0.895 r_chiral_restr 0.125 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2742 Nucleic Acid Atoms Solvent Atoms 456 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement BLU-MAX data collection HKL-3000 data reduction HKL-3000 data scaling PHASER phasing