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Crystal structure of NDM-1 in complex with hydrolyzed ampicillin - new refinement
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q6X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 295 28% (w/v) PEG3350, 0.1 M Bis-Tris, pH 5.8 and 0.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 1.9 35.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.62 α = 90 b = 77.57 β = 90 c = 132.31 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2012-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 2.008 38.785 99.4 26843
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 3q6x 2.01 38.785 25437 1345 97.71 0.13451 0.13192 0.1438 0.18216 0.1879 RANDOM 20.341
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] 1.9 -1.52 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.418 r_dihedral_angle_4_deg 19.261 r_dihedral_angle_3_deg 13.195 r_dihedral_angle_1_deg 6.204 r_long_range_B_other 5.858 r_long_range_B_refined 5.857 r_sphericity_bonded 5.272 r_scangle_other 4.075 r_scbond_it 2.636 r_scbond_other 2.633
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.418 r_dihedral_angle_4_deg 19.261 r_dihedral_angle_3_deg 13.195 r_dihedral_angle_1_deg 6.204 r_long_range_B_other 5.858 r_long_range_B_refined 5.857 r_sphericity_bonded 5.272 r_scangle_other 4.075 r_scbond_it 2.636 r_scbond_other 2.633 r_mcangle_other 2.221 r_mcangle_it 2.219 r_mcbond_it 1.544 r_mcbond_other 1.541 r_angle_refined_deg 1.453 r_angle_other_deg 0.959 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3620 Nucleic Acid Atoms Solvent Atoms 433 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction SCALA data scaling PHASES phasing