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Directed evolutionary changes in MBL super family - NDM-1 Round 10 crystal-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SPU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.75 291 0.1 M MES pH 6.75, 1.3 M MgSO4
Crystal Properties Matthews coefficient Solvent content 1.94 36.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.795 α = 90 b = 137.724 β = 90 c = 77.455 γ = 90
Symmetry Space Group C 2 2 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 210r 2015-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.67 34.45 97.22 0.02929 0.999 17.93 2 23318 19.27
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 1.67 1.73 77.72 0.46 1.89 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 (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 3SPU 1.67 34.45 22123 1195 97.2 0.14659 0.14436 0.1583 0.18687 0.1944 RANDOM 23.277
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] -0.63 -0.22 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.502 r_dihedral_angle_4_deg 22.279 r_dihedral_angle_3_deg 14.469 r_long_range_B_other 7.455 r_long_range_B_refined 7.453 r_dihedral_angle_1_deg 6.419 r_scangle_other 4.175 r_mcangle_it 3.463 r_mcangle_other 3.462 r_scbond_it 2.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.502 r_dihedral_angle_4_deg 22.279 r_dihedral_angle_3_deg 14.469 r_long_range_B_other 7.455 r_long_range_B_refined 7.453 r_dihedral_angle_1_deg 6.419 r_scangle_other 4.175 r_mcangle_it 3.463 r_mcangle_other 3.462 r_scbond_it 2.93 r_scbond_other 2.93 r_mcbond_it 2.327 r_mcbond_other 2.323 r_angle_refined_deg 2.075 r_angle_other_deg 0.984 r_chiral_restr 0.138 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.001 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 1699 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing