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Crystal structure of mycinamicin VIII C21 methyl hydroxylase MycCI from Micromonospora griseorubida bound to mycinamicin VIII
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CV9 PDB ENTRY 3CV9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 20% PEG 3350, 0.2 M CA ACETATE, 20 MM SPERMIDINE, 0.84 MM TCEP, pH 7
Crystal Properties Matthews coefficient Solvent content 2.34 47.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.781 α = 83.2 b = 59.516 β = 72.15 c = 74.623 γ = 62.61
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARRESERCH MIRRORS 2015-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.21 71 91.1 0.24 3.8 2 36326 0.5 31.6
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 2.21 2.33 71.2 1.47 1.3 1.9
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 PDB ENTRY 3CV9 2.21 71 34383 1838 90.81 0.18572 0.18227 0.1893 0.2515 0.2508 RANDOM 27.168
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] 0.27 -0.15 -0.78 -1.47 0.37 1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.67 r_dihedral_angle_4_deg 18.16 r_dihedral_angle_3_deg 15.649 r_dihedral_angle_1_deg 6.595 r_long_range_B_refined 4.87 r_long_range_B_other 4.87 r_scangle_other 3.133 r_mcangle_it 2.886 r_mcangle_other 2.886 r_scbond_it 2.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.67 r_dihedral_angle_4_deg 18.16 r_dihedral_angle_3_deg 15.649 r_dihedral_angle_1_deg 6.595 r_long_range_B_refined 4.87 r_long_range_B_other 4.87 r_scangle_other 3.133 r_mcangle_it 2.886 r_mcangle_other 2.886 r_scbond_it 2.003 r_scbond_other 2.002 r_angle_refined_deg 1.907 r_mcbond_it 1.863 r_mcbond_other 1.862 r_angle_other_deg 1.35 r_chiral_restr 0.109 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 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 6013 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 200
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MrBUMP phasing