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Crystal structure of NDM-1 bound to ethylene glycol
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 298 10% w/v PEG8K, 8% w/v ethylene glycol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.32 47.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.22 α = 90 b = 107.22 β = 90 c = 92.85 γ = 90
Symmetry Space Group P 41 21 2
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 1.47 35.74 99.7 91755 -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 1.47 1.55 98.4
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 1.47 35.74 87439 87107 4592 99.6 0.142 0.14 0.139 0.182 0.1828 RANDOM 17.75
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] 0.27 0.27 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.144 r_dihedral_angle_4_deg 20.428 r_dihedral_angle_3_deg 12.955 r_scangle_it 10.277 r_scbond_it 7.242 r_dihedral_angle_1_deg 6.388 r_mcangle_it 5.339 r_mcbond_it 3.625 r_rigid_bond_restr 3.428 r_angle_refined_deg 2.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.144 r_dihedral_angle_4_deg 20.428 r_dihedral_angle_3_deg 12.955 r_scangle_it 10.277 r_scbond_it 7.242 r_dihedral_angle_1_deg 6.388 r_mcangle_it 5.339 r_mcbond_it 3.625 r_rigid_bond_restr 3.428 r_angle_refined_deg 2.102 r_chiral_restr 0.153 r_bond_refined_d 0.017 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3493 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 12
Software Software Software Name Purpose MxDC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling