6Q4Y

Structure of MPT-2, a GDP-Man-dependent mannosyltransferase from Leishmania mexicana, in complex with mannose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Q50 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP292200 mM trisodium citrate, 18-22% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
33.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.237α = 90
b = 97.138β = 90
c = 105.55γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-12-18MSINGLE 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
11.771.581000.0910.0910.0910.9999.77.76330629.36
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)RedundancyNumber Unique Reflections (All)
11.71.731000.9431.0090.3530.3791.77.8

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 REPLACEMENTTHROUGHOUT6Q501.771.5860031320099.960.176250.174340.21279RANDOM32.108
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]
0.191.27-1.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.592
r_dihedral_angle_4_deg17.972
r_dihedral_angle_3_deg13.897
r_dihedral_angle_1_deg7.456
r_long_range_B_refined6.913
r_long_range_B_other6.884
r_scangle_other4.929
r_mcangle_it3.934
r_mcangle_other3.933
r_scbond_it3.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.592
r_dihedral_angle_4_deg17.972
r_dihedral_angle_3_deg13.897
r_dihedral_angle_1_deg7.456
r_long_range_B_refined6.913
r_long_range_B_other6.884
r_scangle_other4.929
r_mcangle_it3.934
r_mcangle_other3.933
r_scbond_it3.23
r_scbond_other3.23
r_mcbond_it2.696
r_mcbond_other2.694
r_angle_refined_deg1.554
r_angle_other_deg1.377
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms4799
Nucleic Acid Atoms
Solvent Atoms306
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing