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Structure of an inactive variant (D94N) of MPT-2, a GDP-Man-dependent mannosyltransferase from Leishmania mexicana, in complex with beta-1,2-mannobiose
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, HANGING DROP 7 292 200 mM triammonium citrate pH 7.0, 18-22% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.88 34.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.389 α = 90 b = 98.115 β = 90 c = 105.621 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-F 2018-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 1.5 71.89 99.8 0.101 0.109 0.039 0.996 8.1 7.6 92517 19.59
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 97.5 1.26 1.368 0.522 0.629 1.4 6.8
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 6Q4Y 1.55 71.89 79610 4283 99.72 0.12992 0.12683 0.1408 0.18941 0.1983 RANDOM 27.653
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] 0.46 -0.54 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.773 r_dihedral_angle_4_deg 19.271 r_dihedral_angle_3_deg 12.55 r_dihedral_angle_1_deg 7.554 r_long_range_B_refined 5.948 r_long_range_B_other 5.862 r_scangle_other 5.551 r_scbond_it 4.6 r_scbond_other 4.6 r_mcangle_it 4.577
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.773 r_dihedral_angle_4_deg 19.271 r_dihedral_angle_3_deg 12.55 r_dihedral_angle_1_deg 7.554 r_long_range_B_refined 5.948 r_long_range_B_other 5.862 r_scangle_other 5.551 r_scbond_it 4.6 r_scbond_other 4.6 r_mcangle_it 4.577 r_mcangle_other 4.576 r_mcbond_other 3.647 r_mcbond_it 3.646 r_rigid_bond_restr 2.536 r_angle_refined_deg 1.555 r_angle_other_deg 1.393 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4812 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing