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Crystal structure of the MIR domain (aa 337-532) of the S. cerevisiae mannosyltransferase Pmt2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6P25 PDB entry 6P25
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 25% PEG20000 MME
Crystal Properties Matthews coefficient Solvent content 2.09 41.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.289 α = 90 b = 71.403 β = 96.37 c = 37.886 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 100 PIXEL DECTRIS EIGER X 9M 2018-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.078 APS 21-ID-D
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 1.35 37.65 96.7 0.134 13.4 3.5 40003
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 1.35 1.38 0.023
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 6P25 1.35 37.65 36188 1965 95.38 0.187 0.187 0.1959 0.213 0.2219 RANDOM 19.885
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.969 r_dihedral_angle_4_deg 22.167 r_dihedral_angle_3_deg 13.159 r_dihedral_angle_1_deg 8.101 r_long_range_B_refined 7.024 r_long_range_B_other 6.876 r_scangle_other 4.854 r_mcangle_other 3.769 r_mcangle_it 3.768 r_scbond_it 3.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.969 r_dihedral_angle_4_deg 22.167 r_dihedral_angle_3_deg 13.159 r_dihedral_angle_1_deg 8.101 r_long_range_B_refined 7.024 r_long_range_B_other 6.876 r_scangle_other 4.854 r_mcangle_other 3.769 r_mcangle_it 3.768 r_scbond_it 3.168 r_scbond_other 3.167 r_mcbond_it 2.407 r_mcbond_other 2.398 r_angle_refined_deg 2.359 r_angle_other_deg 1.239 r_chiral_restr 0.184 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 r_bond_other_d 0.002 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 1555 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALA data scaling PHASER phasing