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Crystal structure of serratia fonticola SFH-I: Source of the nucleophile in the catalytic mechanism of mono-zinc metallo-beta-lactamases
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X8G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 25% PEG 3350, 0.1M AMMONIUM NITRATE, 3% ISOPROPANOL, PH 7.0
, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.96 37.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.965 α = 90 b = 86.412 β = 90.07 c = 72.193 γ = 90
Symmetry Space Group P 1 21 1
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 315 Mirrors 2008-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9529 Diamond I04
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 1.83 72.2 94 0.07 12.8 2.5 35354 33217
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 1.83 1.9 94.3 0.45 2 2.3 3348
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1X8G 1.83 72.19 31529 1663 93 0.18484 0.18332 0.21311 0.2064 RANDOM 11.27
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] -1.44 -0.76 0.56 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.775 r_dihedral_angle_4_deg 22.005 r_dihedral_angle_3_deg 13.707 r_dihedral_angle_1_deg 6.014 r_sphericity_free 4.18 r_scangle_it 2.811 r_scbond_it 1.892 r_sphericity_bonded 1.778 r_angle_refined_deg 1.334 r_mcangle_it 1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.775 r_dihedral_angle_4_deg 22.005 r_dihedral_angle_3_deg 13.707 r_dihedral_angle_1_deg 6.014 r_sphericity_free 4.18 r_scangle_it 2.811 r_scbond_it 1.892 r_sphericity_bonded 1.778 r_angle_refined_deg 1.334 r_mcangle_it 1.14 r_rigid_bond_restr 1.115 r_mcbond_it 0.735 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3637 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 2
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling