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Crystal structure of NDM-1 bound to hydrolyzed benzylpenicillin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 0.2M MgCl2, 25% PEG3350, 0.1M bis-tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.82 32.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.03 α = 90 b = 79.49 β = 90 c = 134.21 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 RAYONIX MX300HE 2011-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 CLSI 08B1-1
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 1.8 29.7 98.7 39550 39036 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 97.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 1.8 29.7 37675 37046 1952 98.33 0.16445 0.1627 0.1632 0.19735 0.1959 RANDOM 11.505
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] 0.09 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.774 r_dihedral_angle_4_deg 24.075 r_dihedral_angle_3_deg 14.131 r_dihedral_angle_1_deg 7.281 r_scangle_it 5.188 r_scbond_it 3.488 r_mcangle_it 2.098 r_mcbond_it 1.43 r_angle_refined_deg 1.291 r_chiral_restr 0.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.774 r_dihedral_angle_4_deg 24.075 r_dihedral_angle_3_deg 14.131 r_dihedral_angle_1_deg 7.281 r_scangle_it 5.188 r_scbond_it 3.488 r_mcangle_it 2.098 r_mcbond_it 1.43 r_angle_refined_deg 1.291 r_chiral_restr 0.106 r_gen_planes_refined 0.015 r_bond_refined_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3594 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 54
Software Software Software Name Purpose MxDC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling