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Crystal structure of NDM-1 in complex with beta-mercaptoethanol - new refinement
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 10% w/v PEG8K, 8% w/v ethylene glycol, 0.1M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.58 52.3
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 0.97949 CLSI 08B1-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 0.06 10.6 4 91755 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.55 98.4 0.372 3 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 1.47 35.74 87106 4592 99.62 0.11145 0.10956 0.1103 0.14735 0.1479 copied from 4exy 18.599
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] -0.2 -0.2 0.4
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.801 r_dihedral_angle_2_deg 33.301 r_dihedral_angle_4_deg 20.634 r_dihedral_angle_3_deg 12.187 r_sphericity_bonded 12.061 r_long_range_B_refined 5.937 r_long_range_B_other 5.937 r_dihedral_angle_1_deg 5.849 r_scangle_other 4.789 r_scbond_it 4.297
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.801 r_dihedral_angle_2_deg 33.301 r_dihedral_angle_4_deg 20.634 r_dihedral_angle_3_deg 12.187 r_sphericity_bonded 12.061 r_long_range_B_refined 5.937 r_long_range_B_other 5.937 r_dihedral_angle_1_deg 5.849 r_scangle_other 4.789 r_scbond_it 4.297 r_scbond_other 4.296 r_mcangle_other 3.936 r_mcangle_it 3.918 r_mcbond_it 3.113 r_mcbond_other 3.058 r_rigid_bond_restr 2.17 r_angle_refined_deg 1.648 r_angle_other_deg 1.046 r_chiral_restr 0.113 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3497 Nucleic Acid Atoms Solvent Atoms 568 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing