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Crystal structure of ldtMt2 in complex with Faropenem adduct
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VYN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 20% 5000MME, 200mM ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.87 57.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.051 α = 90 b = 93.929 β = 92.72 c = 75.215 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 CCD RIGAKU SATURN 944+ 2014-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.17 50 94.6 0.064 0.056 20.86 3.6 42667
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 2.17 2.21 59.7 0.186 4.19 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 3VYN 2.17 50 40491 2153 95.45 0.18307 0.18036 0.1906 0.23386 0.1928 RANDOM 27.029
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] 0.66 -0.75 1.39 -1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.579 r_dihedral_angle_4_deg 17.548 r_dihedral_angle_3_deg 16.383 r_dihedral_angle_1_deg 7.274 r_long_range_B_refined 5.876 r_long_range_B_other 5.876 r_scangle_other 4.071 r_mcangle_it 2.878 r_mcangle_other 2.878 r_scbond_it 2.748
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.579 r_dihedral_angle_4_deg 17.548 r_dihedral_angle_3_deg 16.383 r_dihedral_angle_1_deg 7.274 r_long_range_B_refined 5.876 r_long_range_B_other 5.876 r_scangle_other 4.071 r_mcangle_it 2.878 r_mcangle_other 2.878 r_scbond_it 2.748 r_scbond_other 2.743 r_mcbond_it 1.954 r_mcbond_other 1.954 r_angle_refined_deg 1.929 r_angle_other_deg 1.079 r_chiral_restr 0.128 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 5292 Nucleic Acid Atoms Solvent Atoms 462 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement PHASER phasing HKL-3000 data reduction SCALA data scaling