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Crystal structure of NDM-1 bound to hydrolyzed meropenem
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 298 1M trisodium cacodylate, 0.1M sodium cacodylate , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.26 45.63
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 40390 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 92.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 1.9 42.19 39990 38311 2030 95.8 0.186 0.184 0.1906 0.224 0.2318 RANDOM 17.86
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] 0.28 0.28 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.826 r_dihedral_angle_4_deg 21.11 r_dihedral_angle_3_deg 14.474 r_dihedral_angle_1_deg 7.638 r_scangle_it 6.419 r_scbond_it 4.453 r_mcangle_it 2.845 r_angle_refined_deg 1.977 r_mcbond_it 1.888 r_chiral_restr 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.826 r_dihedral_angle_4_deg 21.11 r_dihedral_angle_3_deg 14.474 r_dihedral_angle_1_deg 7.638 r_scangle_it 6.419 r_scbond_it 4.453 r_mcangle_it 2.845 r_angle_refined_deg 1.977 r_mcbond_it 1.888 r_chiral_restr 0.125 r_gen_planes_refined 0.019 r_bond_refined_d 0.013 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3500 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 58
Software Software Software Name Purpose MxDC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling