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Amide bond synthetase from Streptomyces hindustanus K492H mutant in complex with Adenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SQ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.2 M Li2SO4; 0.1 M HEPES pH 7.5; 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.8 56.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.167 α = 90 b = 96.159 β = 117.74 c = 87.323 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 120 PIXEL DECTRIS EIGER2 XE 16M 2022-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.95881 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 2.02 29.35 99 0.12 0.06 1 11.6 7 78528 26
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 2.02 2.06 1.05 0.55 0.8 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.02 29.35 74561 3938 98.98 0.22632 0.22442 0.2328 0.26231 0.2696 RANDOM 30.238
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] -0.8 -0.11 1.69 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.542 r_dihedral_angle_2_deg 10.673 r_dihedral_angle_1_deg 7.17 r_long_range_B_refined 6.242 r_long_range_B_other 6.2 r_scangle_other 4.772 r_mcangle_it 3.759 r_mcangle_other 3.759 r_scbond_it 3.156 r_scbond_other 3.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.542 r_dihedral_angle_2_deg 10.673 r_dihedral_angle_1_deg 7.17 r_long_range_B_refined 6.242 r_long_range_B_other 6.2 r_scangle_other 4.772 r_mcangle_it 3.759 r_mcangle_other 3.759 r_scbond_it 3.156 r_scbond_other 3.14 r_mcbond_it 2.701 r_mcbond_other 2.7 r_angle_refined_deg 1.398 r_angle_other_deg 0.469 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 7393 Nucleic Acid Atoms Solvent Atoms 513 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing