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Crystal Structure of DIM-1 metallo-beta-lactamase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DDK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20% polyethylene glycol (PEG) 550 monomethyl ether (MME), 10% PEG 20000, 50 mM HEPES / 50 mM MOPS pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.91 35.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.719 α = 90 b = 47.856 β = 90 c = 185.216 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 ADSC QUANTUM 4 2009-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 50 94.5 0.051 32.5 7.1 21133
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 68.4 0.251 6.6 5.9
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 1DDK 2.2 42.55 20006 1095 94.53 0.20989 0.20654 0.2151 0.27397 0.2786 RANDOM 51.26
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] -1.37 0.07 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.568 r_dihedral_angle_4_deg 17.078 r_dihedral_angle_3_deg 16.526 r_long_range_B_refined 7.064 r_long_range_B_other 6.92 r_dihedral_angle_1_deg 6.916 r_mcangle_it 3.184 r_mcangle_other 3.183 r_scangle_other 2.862 r_mcbond_other 2.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.568 r_dihedral_angle_4_deg 17.078 r_dihedral_angle_3_deg 16.526 r_long_range_B_refined 7.064 r_long_range_B_other 6.92 r_dihedral_angle_1_deg 6.916 r_mcangle_it 3.184 r_mcangle_other 3.183 r_scangle_other 2.862 r_mcbond_other 2.079 r_mcbond_it 2.078 r_scbond_it 1.843 r_scbond_other 1.843 r_angle_refined_deg 1.617 r_angle_other_deg 0.84 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3392 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction Coot model building