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Crystal structure of NDM-1 at pH7.3 (HEPES) in complex with hydrolyzed ampicillin
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 7.3 295 0.1M HEPES pH7.3, 20% PEG 3350, 20mg/ml ampicillin
Crystal Properties Matthews coefficient Solvent content 2.03 39.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.142 α = 90 b = 79.215 β = 90 c = 134.141 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 CCD ADSC QUANTUM 315r 2011-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97922 SSRF BL17U1
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 1.15 50 93.4 0.074 8.4 6.1 139092
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 1.15 1.19 91 0.514 6.3
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 1.15 50 132045 6951 93.04 0.13 0.129 0.1344 0.1476 0.1509 RANDOM 17.641
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] -0.02 0.07 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.534 r_sphericity_free 22.105 r_dihedral_angle_4_deg 16.859 r_dihedral_angle_3_deg 11.362 r_sphericity_bonded 7.708 r_rigid_bond_restr 6.337 r_dihedral_angle_1_deg 6.15 r_angle_refined_deg 1.31 r_angle_other_deg 0.804 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.534 r_sphericity_free 22.105 r_dihedral_angle_4_deg 16.859 r_dihedral_angle_3_deg 11.362 r_sphericity_bonded 7.708 r_rigid_bond_restr 6.337 r_dihedral_angle_1_deg 6.15 r_angle_refined_deg 1.31 r_angle_other_deg 0.804 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3598 Nucleic Acid Atoms Solvent Atoms 698 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction