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Structure of MPT-1, a GDP-Man-dependent mannosyltransferase from Leishmania mexicana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Q4Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 12% w/v PEG 20K, 100 mM MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.07 40.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.478 α = 94.48 b = 48.116 β = 96.92 c = 73.887 γ = 110.29
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 PILATUS3 6M 2018-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 1.55 72.74 94.5 0.09 0.119 0.076 0.97 4.5 2.1 80753 13.86
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 1.55 1.58 90.8 0.357 0.47 0.304 0.782 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 6Q4Y 1.55 72.74 76774 3977 94.45 0.15258 0.14943 0.1511 0.21339 0.2163 RANDOM 19.002
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] 0.86 -0.6 -1.59 0.57 -1.73 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.985 r_dihedral_angle_3_deg 13.148 r_dihedral_angle_4_deg 12.511 r_dihedral_angle_1_deg 7.294 r_rigid_bond_restr 6.002 r_long_range_B_refined 5.818 r_long_range_B_other 5.461 r_scangle_other 5.036 r_scbond_it 4.291 r_scbond_other 4.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.985 r_dihedral_angle_3_deg 13.148 r_dihedral_angle_4_deg 12.511 r_dihedral_angle_1_deg 7.294 r_rigid_bond_restr 6.002 r_long_range_B_refined 5.818 r_long_range_B_other 5.461 r_scangle_other 5.036 r_scbond_it 4.291 r_scbond_other 4.291 r_mcangle_it 3.771 r_mcangle_other 3.771 r_mcbond_it 3.246 r_mcbond_other 3.243 r_angle_refined_deg 1.767 r_angle_other_deg 1.475 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4852 Nucleic Acid Atoms Solvent Atoms 606 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing