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Structure of amide bond synthetase Mcba K483A mutant from Marinactinospora thermotolerans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GXQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 1. 6 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.86 56.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.234 α = 90 b = 130.738 β = 90 c = 196.383 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 120 PIXEL DECTRIS PILATUS3 S 6M 2018-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97624 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.8 108.83 100 0.26 0.11 0.99 8.3 13.2 75674
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.86 1.13 0.46 0.67 2.6
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 4GXQ 2.8 101.5 71980 3618 100 0.20605 0.20396 0.24775 0.2254 RANDOM 49.194
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] 2.69 1.97 -4.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.354 r_dihedral_angle_4_deg 20.33 r_dihedral_angle_3_deg 18.645 r_long_range_B_refined 9.792 r_long_range_B_other 9.792 r_dihedral_angle_1_deg 7 r_scangle_other 6.857 r_mcangle_it 6.798 r_mcangle_other 6.797 r_scbond_it 4.479
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.354 r_dihedral_angle_4_deg 20.33 r_dihedral_angle_3_deg 18.645 r_long_range_B_refined 9.792 r_long_range_B_other 9.792 r_dihedral_angle_1_deg 7 r_scangle_other 6.857 r_mcangle_it 6.798 r_mcangle_other 6.797 r_scbond_it 4.479 r_scbond_other 4.479 r_mcbond_it 4.412 r_mcbond_other 4.412 r_angle_refined_deg 1.368 r_angle_other_deg 0.879 r_chiral_restr 0.063 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 17686 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 206
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing