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Structure of MPT-2, a GDP-Man-dependent mannosyltransferase from Leishmania mexicana, in complex with mannose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Q50
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 200 mM trisodium citrate, 18-22% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 33.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.237 α = 90 b = 97.138 β = 90 c = 105.55 γ = 90
Symmetry Space Group P 21 21 21
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 2017-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.7 71.58 100 0.091 0.091 0.091 0.999 9.7 7.7 63306 29.36
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 1.7 1.73 100 0.943 1.009 0.353 0.379 1.7 7.8
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 6Q50 1.7 71.58 60031 3200 99.96 0.17625 0.17434 0.1829 0.21279 0.2207 RANDOM 32.108
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] 0.19 1.27 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.592 r_dihedral_angle_4_deg 17.972 r_dihedral_angle_3_deg 13.897 r_dihedral_angle_1_deg 7.456 r_long_range_B_refined 6.913 r_long_range_B_other 6.884 r_scangle_other 4.929 r_mcangle_it 3.934 r_mcangle_other 3.933 r_scbond_it 3.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.592 r_dihedral_angle_4_deg 17.972 r_dihedral_angle_3_deg 13.897 r_dihedral_angle_1_deg 7.456 r_long_range_B_refined 6.913 r_long_range_B_other 6.884 r_scangle_other 4.929 r_mcangle_it 3.934 r_mcangle_other 3.933 r_scbond_it 3.23 r_scbond_other 3.23 r_mcbond_it 2.696 r_mcbond_other 2.694 r_angle_refined_deg 1.554 r_angle_other_deg 1.377 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 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 4799 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing