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Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed compound 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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 1.8 31.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.114 α = 90 b = 78.847 β = 90 c = 133.534 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 PILATUS 6M 2022-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97915 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.89 27.77 98.86 0.121 0.997 22.92 12.5 33742 18.47
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 1.9 1.93 0.937
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.89 27.77 1.34 33742 1738 98.86 0.1529 0.151 0.1511 0.1895 0.19 22.79
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 6.3308 f_angle_d 0.9455 f_chiral_restr 0.0593 f_bond_d 0.0073 f_plane_restr 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3568 Nucleic Acid Atoms Solvent Atoms 558 Heterogen Atoms 62
Software Software Software Name Purpose HKL-3000 data reduction HKL-3000 data scaling Coot model building PHENIX phasing PHENIX refinement