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Structure of the Laspartomycin C double mutant G4D D-allo-Thr9D-Dap in complex with Geranyl phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5O0Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.2 M sodium formate, 40% MPD
Crystal Properties Matthews coefficient Solvent content 2.4 48.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.428 α = 90 b = 40.428 β = 90 c = 31.033 γ = 120
Symmetry Space Group P 6 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2019-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
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 1.031 35.012 92.2 0.185 0.193 0.054 0.997 8 11.7 6321
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 1.031 1.116 53.1 1.584 1.664 0.504 0.726 1.5 10.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5O0Z 1.04 35.01 6011 299 82.66 0.1215 0.1204 0.123 0.1432 0.1448 RANDOM 16.751
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] 0.69 0.35 0.69 -2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 67.91 r_dihedral_angle_2_deg 24.766 r_dihedral_angle_3_deg 12.913 r_rigid_bond_restr 2.465 r_angle_refined_deg 1.721 r_angle_other_deg 0.662 r_chiral_restr 0.109 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 67.91 r_dihedral_angle_2_deg 24.766 r_dihedral_angle_3_deg 12.913 r_rigid_bond_restr 2.465 r_angle_refined_deg 1.721 r_angle_other_deg 0.662 r_chiral_restr 0.109 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 91 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement PHASER phasing Aimless data scaling STARANISO data scaling DIALS data reduction