6Q50

Structure of MPT-4, a mannose phosphorylase from Leishmania mexicana, in complex with phosphate ion


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B4W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7293100 mM PCTP pH 7.0, 25% w/v PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.3146.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.366α = 90
b = 67.194β = 90
c = 96.97γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.969DiamondI24

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
11.667.191000.1040.1110.0390.99810.284682920.08
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)
11.61.631001.8531.9850.7040.4598

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 REPLACEMENTTHROUGHOUT2B4W1.667.2844419236099.960.162410.160480.20006RANDOM23.552
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]
0.16-0.60.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.122
r_dihedral_angle_4_deg16.216
r_dihedral_angle_1_deg14.669
r_dihedral_angle_3_deg13.445
r_long_range_B_refined6.504
r_long_range_B_other6.385
r_scangle_other4.811
r_scbond_it3.198
r_scbond_other3.19
r_mcangle_it2.954
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.122
r_dihedral_angle_4_deg16.216
r_dihedral_angle_1_deg14.669
r_dihedral_angle_3_deg13.445
r_long_range_B_refined6.504
r_long_range_B_other6.385
r_scangle_other4.811
r_scbond_it3.198
r_scbond_other3.19
r_mcangle_it2.954
r_mcangle_other2.954
r_mcbond_other2.063
r_mcbond_it2.062
r_angle_refined_deg1.742
r_angle_other_deg1.435
r_chiral_restr0.089
r_bond_refined_d0.012
r_gen_planes_refined0.01
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 Atoms2519
Nucleic Acid Atoms
Solvent Atoms373
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing