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R39-imipenem Acyl-enzyme crystal structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W8Q PDB ENTRY 1W8Q
Crystallization Crystal Properties Matthews coefficient Solvent content 2.48 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.623 α = 90 b = 91.911 β = 94.5 c = 106.924 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 ADSC CCD 2011-04-16 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 2.15 25.7 99.8 0.08 10 3.5 108662
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 2.15 2.27 99.4 0.49 2.5 3.5
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 1W8Q 2.15 35.72 103175 5420 99.77 0.18951 0.18719 0.1866 0.23441 0.2339 RANDOM 43.552
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] -0.03 0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.535 r_dihedral_angle_4_deg 16.571 r_dihedral_angle_3_deg 12.958 r_dihedral_angle_1_deg 5.905 r_scangle_it 3.765 r_scbond_it 2.274 r_mcangle_it 1.588 r_angle_refined_deg 1.366 r_mcbond_it 0.862 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.535 r_dihedral_angle_4_deg 16.571 r_dihedral_angle_3_deg 12.958 r_dihedral_angle_1_deg 5.905 r_scangle_it 3.765 r_scbond_it 2.274 r_mcangle_it 1.588 r_angle_refined_deg 1.366 r_mcbond_it 0.862 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13394 Nucleic Acid Atoms Solvent Atoms 970 Heterogen Atoms 273
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling