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Structure of a borosin methyltransferase from Mycena rosella with native peptide (MroMA1) in complex with SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N0S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 282 5% PEG 3350, 200 mM ammonium acetate and 100 mM Tris-HCl buffer (pH=8.5)
Crystal Properties Matthews coefficient Solvent content 2.83 56.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 191.833 α = 90 b = 191.833 β = 90 c = 93.709 γ = 120
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 2019-11-24 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) 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 1.79 96 100 0.099 0.999 21.2 15.8 183361
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 1.79 1.8 100 1.326 2
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 5N0S 1.79 25 174260 9013 99.9 0.168 0.167 0.1685 0.192 0.1943 RANDOM 30.62
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] 0.47 0.24 0.47 -1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.053 r_dihedral_angle_4_deg 21.225 r_dihedral_angle_3_deg 12.894 r_dihedral_angle_1_deg 5.736 r_angle_refined_deg 1.053 r_chiral_restr 0.084 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.053 r_dihedral_angle_4_deg 21.225 r_dihedral_angle_3_deg 12.894 r_dihedral_angle_1_deg 5.736 r_angle_refined_deg 1.053 r_chiral_restr 0.084 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11793 Nucleic Acid Atoms Solvent Atoms 1624 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction autoPROC data scaling PHASER phasing