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Structure of New Delhi Metallo-Beta-lactamase 1 (NDM-1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WHG PDB ENTRY 2WHG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 5 MM COCL2, 5 MM NICL2, 5 MM MGCL2, 5 MM CDCL2, 100 MM HEPES PH 7.5, 12% (W/V) PEG 3350.
Crystal Properties Matthews coefficient Solvent content 3.28 62.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.3 α = 90 b = 120.3 β = 90 c = 88.1 γ = 90
Symmetry Space Group I 4 2 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 ADSC CCD 2011-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.91 28.79 99.8 0.07 26.3 13.3 25258 2 64.1
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 1.91 1.96 97.6 0.76 3.3 12.2
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 2WHG 1.91 19.56 23970 1288 100 0.1815 0.18001 0.196 0.20956 0.2206 RANDOM 32.772
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.61 r_dihedral_angle_4_deg 16.528 r_dihedral_angle_3_deg 14.495 r_dihedral_angle_1_deg 8.3 r_scangle_it 4.538 r_scbond_it 3.249 r_mcangle_it 2.221 r_angle_refined_deg 1.577 r_mcbond_it 1.556 r_chiral_restr 0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.61 r_dihedral_angle_4_deg 16.528 r_dihedral_angle_3_deg 14.495 r_dihedral_angle_1_deg 8.3 r_scangle_it 4.538 r_scbond_it 3.249 r_mcangle_it 2.221 r_angle_refined_deg 1.577 r_mcbond_it 1.556 r_chiral_restr 0.141 r_bond_refined_d 0.019 r_gen_planes_refined 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_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 1696 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing