6Q4X

Structure of MPT-2, a GDP-Man-dependent mannosyltransferase from Leishmania mexicana


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP292200 mM trisodium citrate, 18-22% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.9336.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.567α = 90
b = 98.607β = 90
c = 107.402γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.5572.7498.30.1030.1130.0450.9977.15.98494020.42
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)RedundancyNumber Unique Reflections (All)
11.551.5881.10.7560.8590.3950.433.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.5572.7480530432898.30.14360.140050.21091RANDOM28.953
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]
-3.570.33.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.885
r_dihedral_angle_4_deg17.769
r_dihedral_angle_3_deg13.682
r_long_range_B_refined8.126
r_long_range_B_other8.002
r_scangle_other7.58
r_dihedral_angle_1_deg7.179
r_scbond_it6.265
r_scbond_other6.265
r_mcangle_it6.237
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.885
r_dihedral_angle_4_deg17.769
r_dihedral_angle_3_deg13.682
r_long_range_B_refined8.126
r_long_range_B_other8.002
r_scangle_other7.58
r_dihedral_angle_1_deg7.179
r_scbond_it6.265
r_scbond_other6.265
r_mcangle_it6.237
r_mcangle_other6.236
r_rigid_bond_restr5.769
r_mcbond_it5.243
r_mcbond_other5.243
r_angle_refined_deg1.575
r_angle_other_deg1.516
r_chiral_restr0.084
r_bond_refined_d0.012
r_bond_other_d0.012
r_gen_planes_refined0.008
r_gen_planes_other0.004
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 AtomsNumber
Protein Atoms4936
Nucleic Acid Atoms
Solvent Atoms638
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing