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NDM1-inhibitor co-structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZR9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2 M ammonium acetate
0.1 M sodium acetate pH 4.6
20.0 w/v polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 1.97 37.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.03 α = 90 b = 78.81 β = 90 c = 134.81 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 2012-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1. APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 0.99 134.805 94.1 0.042 0.056 0.022 23.9 6.5 217293 217293 5.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.99 1.02 81.3 0.322 0.322 0.386 0.16 2.2 5.3
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 3ZR9 0.99 14.49 217086 10920 93.89 0.1372 0.1366 0.14 0.1482 0.1515 RANDOM 11.84
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] 0.5057 -0.0682 -0.4375
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.45 t_omega_torsion 5.24 t_angle_deg 1.12 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.45 t_omega_torsion 5.24 t_angle_deg 1.12 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3568 Nucleic Acid Atoms Solvent Atoms 702 Heterogen Atoms 57
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling PDB_EXTRACT data extraction BUSTER phasing