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Crystal Structure of Vibrio cholerae Methionine Aminopeptidase with Partially Occupied Metals
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6K26
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 298 0.1 M Hepes pH-7.3 , 10% PEG 3350, 5% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.39 49.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.702 α = 90 b = 50.293 β = 97.241 c = 131.684 γ = 90
Symmetry Space Group P 1 21 1
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 2019-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.9536 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.47 49.31 99.7 0.062 0.067 0.026 0.999 17.6 6.3 108944
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.5 97.7 0.676 0.739 0.294 0.841 6
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6K26 1.473 48.226 108924 5364 99.646 0.153 0.1518 0.1765 0.1762 15.882
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] -0.755 0.026 0.544 0.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.056 r_dihedral_angle_4_deg 18.751 r_dihedral_angle_3_deg 10.782 r_dihedral_angle_1_deg 6.624 r_lrange_it 5.113 r_lrange_other 5.072 r_scangle_it 4.26 r_scangle_other 4.252 r_scbond_it 2.831 r_scbond_other 2.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.056 r_dihedral_angle_4_deg 18.751 r_dihedral_angle_3_deg 10.782 r_dihedral_angle_1_deg 6.624 r_lrange_it 5.113 r_lrange_other 5.072 r_scangle_it 4.26 r_scangle_other 4.252 r_scbond_it 2.831 r_scbond_other 2.805 r_mcangle_other 2.071 r_mcangle_it 2.069 r_angle_refined_deg 1.883 r_angle_other_deg 1.51 r_mcbond_it 1.467 r_mcbond_other 1.463 r_xyhbond_nbd_other 0.311 r_nbd_refined 0.225 r_symmetry_xyhbond_nbd_refined 0.217 r_nbd_other 0.194 r_symmetry_nbd_other 0.186 r_metal_ion_refined 0.177 r_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.167 r_symmetry_nbd_refined 0.138 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_other 0.058 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4378 Nucleic Acid Atoms Solvent Atoms 550 Heterogen Atoms 30
Software Software Software Name Purpose Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction