☰ Navigation Tabs
Crystal structure of metallo-beta-lactamase IMP-1 mutant (D81A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DD6 PDB ENTRY 1DD6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 297 acetic-acetate, citrate, PEG4000, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.75 54.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.734 α = 85.37 b = 73.016 β = 75.53 c = 82.45 γ = 73.62
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00 SPring-8 BL41XU
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 2.01 50 67829 67829 14.7
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 2.01 2.08
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DD6 2.01 46.35 67829 1845 94.9 0.212 0.212 0.218 RANDOM 30.6
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] -7.79 -5.28 -2.02 9.36 5.99 -1.57
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.9 c_scangle_it 4.92 c_mcangle_it 4.32 c_scbond_it 4.31 c_mcbond_it 3.98 c_angle_deg 2 c_improper_angle_d 1.46 c_bond_d 0.023 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.9 c_scangle_it 4.92 c_mcangle_it 4.32 c_scbond_it 4.31 c_mcbond_it 3.98 c_angle_deg 2 c_improper_angle_d 1.46 c_bond_d 0.023 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6844 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 20
Software Software Software Name Purpose DENZO data reduction AMoRE phasing CNS refinement