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Crystal structure of New Delhi Metallo-beta-lactamase (NDM-1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WRS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 20mM CdCl2, 20mM CaCl2, 20mM CoCl2, 20% (v/w) PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.18 43.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.696 α = 90 b = 40.696 β = 90 c = 215.292 γ = 120
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 QUANTUM 270 2011-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
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 2.5 50 71.3 10177
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 2WRS 2.5 30 9265 502 70.89 0.2359 0.23425 0.2339 0.26742 0.2679 RANDOM 18.773
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] -0.91 -0.45 -0.91 1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.721 r_dihedral_angle_3_deg 24.402 r_dihedral_angle_4_deg 17.242 r_dihedral_angle_1_deg 9.195 r_scangle_it 2.163 r_angle_refined_deg 1.785 r_scbond_it 1.455 r_mcangle_it 0.892 r_mcbond_it 0.529 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.721 r_dihedral_angle_3_deg 24.402 r_dihedral_angle_4_deg 17.242 r_dihedral_angle_1_deg 9.195 r_scangle_it 2.163 r_angle_refined_deg 1.785 r_scbond_it 1.455 r_mcangle_it 0.892 r_mcbond_it 0.529 r_chiral_restr 0.112 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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 3240 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 4
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling