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Structure of MPT-2, a GDP-Man-dependent mannosyltransferase from Leishmania mexicana
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 1.93 36.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.567 α = 90 b = 98.607 β = 90 c = 107.402 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 2017-12-17 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 1.55 72.74 98.3 0.103 0.113 0.045 0.997 7.1 5.9 84940 20.42
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 81.1 0.756 0.859 0.395 0.43 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.55 72.74 80530 4328 98.3 0.1436 0.14005 0.1528 0.21091 0.2225 RANDOM 28.953
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] -3.57 0.3 3.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.885 r_dihedral_angle_4_deg 17.769 r_dihedral_angle_3_deg 13.682 r_long_range_B_refined 8.126 r_long_range_B_other 8.002 r_scangle_other 7.58 r_dihedral_angle_1_deg 7.179 r_scbond_it 6.265 r_scbond_other 6.265 r_mcangle_it 6.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.885 r_dihedral_angle_4_deg 17.769 r_dihedral_angle_3_deg 13.682 r_long_range_B_refined 8.126 r_long_range_B_other 8.002 r_scangle_other 7.58 r_dihedral_angle_1_deg 7.179 r_scbond_it 6.265 r_scbond_other 6.265 r_mcangle_it 6.237 r_mcangle_other 6.236 r_rigid_bond_restr 5.769 r_mcbond_it 5.243 r_mcbond_other 5.243 r_angle_refined_deg 1.575 r_angle_other_deg 1.516 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_bond_other_d 0.012 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 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 4936 Nucleic Acid Atoms Solvent Atoms 638 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing