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Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed penicillin V
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RL2 4RL2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.1M Succinate pH5.5, 32%PEG3350
Crystal Properties Matthews coefficient Solvent content 1.82 32.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.14 α = 90 b = 79.05 β = 90 c = 134.28 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 PIXEL DECTRIS PILATUS3 6M 2021-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.4 35.08 96.2 0.997 16.32 10.2 79892 11.58
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 0.897
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4RL2 1.4 35.08 1.42 79878 4081 96.24 0.1258 0.124 0.1252 0.1599 0.1614 17.58
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.1973 f_angle_d 1.1313 f_chiral_restr 0.0945 f_plane_restr 0.0092 f_bond_d 0.0086
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3576 Nucleic Acid Atoms Solvent Atoms 638 Heterogen Atoms 55
Software Software Software Name Purpose XDS data reduction XDS data scaling Coot model building PHENIX phasing PHENIX refinement