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Crystal structure of metallo-beta-lactamase IMP-6.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DD6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 297 Hepes, sodium acetate, sodium citrate, PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.88 57.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.799 α = 83.446 b = 76.098 β = 75.317 c = 82.114 γ = 74.063
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 315r 2013-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.954 50 92.9 0.089 20 3 75127
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 1.96 1.99 66.4 0.172 3.1 2.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1DD6 1.954 35.415 75080 3754 92.517 0.192 0.1899 0.1944 0.2263 0.2265 31.882
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] 0.001 0.001 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.138 r_dihedral_angle_4_deg 22.248 r_dihedral_angle_3_deg 14.841 r_dihedral_angle_1_deg 7.053 r_lrange_other 6.008 r_lrange_it 6.006 r_scangle_it 3.87 r_scangle_other 3.87 r_mcangle_other 3.395 r_mcangle_it 3.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.138 r_dihedral_angle_4_deg 22.248 r_dihedral_angle_3_deg 14.841 r_dihedral_angle_1_deg 7.053 r_lrange_other 6.008 r_lrange_it 6.006 r_scangle_it 3.87 r_scangle_other 3.87 r_mcangle_other 3.395 r_mcangle_it 3.394 r_scbond_it 2.317 r_scbond_other 2.315 r_mcbond_it 2.05 r_mcbond_other 2.047 r_angle_refined_deg 1.345 r_angle_other_deg 1.191 r_nbd_refined 0.196 r_nbd_other 0.193 r_symmetry_nbd_refined 0.172 r_symmetry_nbd_other 0.17 r_nbtor_refined 0.158 r_xyhbond_nbd_refined 0.135 r_symmetry_xyhbond_nbd_refined 0.113 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.062 r_metal_ion_refined 0.051 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6780 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 8
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling AMoRE phasing REFMAC refinement PHENIX refinement Coot model building