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Crystal structure of the OXA-10 V117T mutant at pH 8.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K4F PDB ENTRY 1K4F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 1.8 M AS BUFFER HEPES 0.1 M PH 8.0
Crystal Properties Matthews coefficient Solvent content 2.29 45.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.65 α = 90 b = 96.62 β = 90 c = 126.02 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 ADSC CCD 2008-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 1.8 48.62 99.2 0.07 19.9 7 55385 13.45
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 1.8 1.9 94.5 0.21 7.7 5.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1K4F 1.8 38.52 52492 2808 99.1 0.151 0.149 0.1478 0.187 0.1863 RANDOM 14.418
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] -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.065 r_dihedral_angle_4_deg 17.319 r_dihedral_angle_3_deg 13.417 r_dihedral_angle_1_deg 5.127 r_sphericity_free 4.073 r_scangle_it 3.818 r_scbond_it 2.492 r_sphericity_bonded 2.116 r_mcangle_it 1.66 r_rigid_bond_restr 1.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.065 r_dihedral_angle_4_deg 17.319 r_dihedral_angle_3_deg 13.417 r_dihedral_angle_1_deg 5.127 r_sphericity_free 4.073 r_scangle_it 3.818 r_scbond_it 2.492 r_sphericity_bonded 2.116 r_mcangle_it 1.66 r_rigid_bond_restr 1.513 r_angle_refined_deg 1.34 r_mcbond_it 1.115 r_nbtor_refined 0.301 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.182 r_xyhbond_nbd_refined 0.14 r_symmetry_hbond_refined 0.135 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3902 Nucleic Acid Atoms Solvent Atoms 517 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling AMoRE phasing