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Crystal structure of NDM-1 in complex with hydrolyzed meropenem - new refinement
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 1M trisodium cacodylate, 0.1M sodium cacodylate , pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.5 50.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106 α = 90 b = 106 β = 90 c = 92.58 γ = 90
Symmetry Space Group P 41 21 2
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 RAYONIX MX300HE 2011-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 CLSI 08B1-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 42.19 96.1 999 999 40390 -3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 1.9 42.19 38308 2030 95.79 0.157 0.1547 0.1662 0.20008 0.2123 copied from 4eyl 20.141
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] 0.05 0.05 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.478 r_dihedral_angle_4_deg 19.595 r_dihedral_angle_3_deg 13.398 r_long_range_B_refined 6.692 r_long_range_B_other 6.692 r_dihedral_angle_1_deg 6.416 r_angle_other_deg 4.256 r_scangle_other 4.087 r_mcangle_it 2.809 r_mcangle_other 2.809
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.478 r_dihedral_angle_4_deg 19.595 r_dihedral_angle_3_deg 13.398 r_long_range_B_refined 6.692 r_long_range_B_other 6.692 r_dihedral_angle_1_deg 6.416 r_angle_other_deg 4.256 r_scangle_other 4.087 r_mcangle_it 2.809 r_mcangle_other 2.809 r_scbond_it 2.639 r_scbond_other 2.638 r_mcbond_it 1.812 r_mcbond_other 1.803 r_angle_refined_deg 1.797 r_chiral_restr 0.109 r_gen_planes_other 0.054 r_bond_refined_d 0.044 r_gen_planes_refined 0.014 r_bond_other_d 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 3510 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement