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Lysinoalanine synthase, DurN, from duramycin biosynthesis bound to duramycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C0H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 22.5% PEG 3350, 0.1 M MES pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.01 38.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.881 α = 71.51 b = 67.423 β = 76.25 c = 69.122 γ = 72.92
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 RAYONIX MX-300 2017-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.658 64.72 95.8 0.072 0.082 0.039 0.998 12 4.4 109913
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.658 1.687 95.5 0.726 0.823 0.387 0.781 2.1 4.4
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 6C0H 1.66 64.72 104658 5255 95.75 0.18719 0.18437 0.1981 0.24231 0.2477 RANDOM 21.92
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] 0.11 -0.04 -0.45 -1.14 0.61 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.047 r_dihedral_angle_4_deg 15.291 r_dihedral_angle_3_deg 14.559 r_long_range_B_refined 7.056 r_long_range_B_other 6.502 r_dihedral_angle_1_deg 6.043 r_scangle_other 4.488 r_scbond_it 2.946 r_scbond_other 2.946 r_mcangle_it 2.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.047 r_dihedral_angle_4_deg 15.291 r_dihedral_angle_3_deg 14.559 r_long_range_B_refined 7.056 r_long_range_B_other 6.502 r_dihedral_angle_1_deg 6.043 r_scangle_other 4.488 r_scbond_it 2.946 r_scbond_other 2.946 r_mcangle_it 2.85 r_mcangle_other 2.85 r_angle_refined_deg 2.119 r_mcbond_it 2.027 r_mcbond_other 2.026 r_angle_other_deg 1.315 r_chiral_restr 0.138 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 7800 Nucleic Acid Atoms Solvent Atoms 1223 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing