6Q4W

Structure of MPT-1, a GDP-Man-dependent mannosyltransferase from Leishmania mexicana


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Q4Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529212% w/v PEG 20K, 100 mM MES pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.0740.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.478α = 94.48
b = 48.116β = 96.92
c = 73.887γ = 110.29
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

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
11.5572.7494.50.090.1190.0760.974.52.18075313.86
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)RedundancyNumber Unique Reflections (All)
11.551.5890.80.3570.470.3040.7821.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT6Q4Y1.5572.7476774397794.450.152580.149430.21339RANDOM19.002
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]
0.86-0.6-1.590.57-1.730.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.985
r_dihedral_angle_3_deg13.148
r_dihedral_angle_4_deg12.511
r_dihedral_angle_1_deg7.294
r_rigid_bond_restr6.002
r_long_range_B_refined5.818
r_long_range_B_other5.461
r_scangle_other5.036
r_scbond_it4.291
r_scbond_other4.291
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.985
r_dihedral_angle_3_deg13.148
r_dihedral_angle_4_deg12.511
r_dihedral_angle_1_deg7.294
r_rigid_bond_restr6.002
r_long_range_B_refined5.818
r_long_range_B_other5.461
r_scangle_other5.036
r_scbond_it4.291
r_scbond_other4.291
r_mcangle_it3.771
r_mcangle_other3.771
r_mcbond_it3.246
r_mcbond_other3.243
r_angle_refined_deg1.767
r_angle_other_deg1.475
r_chiral_restr0.088
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms4852
Nucleic Acid Atoms
Solvent Atoms606
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing