5MPO

Crystal structure of human molybdopterin synthase complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Q5W2Q5W:D, 4AP8:A
experimental modelPDB 4AP82Q5W:D, 4AP8:A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP28312% PEG3350 -- 0.1M potassium nitrate -- 0.05M potassium thiocyanate
Crystal Properties
Matthews coefficientSolvent content
3.6164.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.72α = 90
b = 123.72β = 90
c = 82.49γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97626DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
12.4361.8699.90.0620.02815.86.827171
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.432.491000.9550.4720.6351.66.1

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 REPLACEMENTTHROUGHOUT2Q5W:D, 4AP8:A2.4361.8625929121799.910.207180.204870.2586RANDOM59.537
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]
-1.51-0.76-1.514.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.772
r_dihedral_angle_4_deg19.978
r_dihedral_angle_3_deg15.439
r_long_range_B_refined9.699
r_long_range_B_other9.697
r_scangle_other7.923
r_dihedral_angle_1_deg7.139
r_mcangle_it6.931
r_mcangle_other6.929
r_scbond_it5.634
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.772
r_dihedral_angle_4_deg19.978
r_dihedral_angle_3_deg15.439
r_long_range_B_refined9.699
r_long_range_B_other9.697
r_scangle_other7.923
r_dihedral_angle_1_deg7.139
r_mcangle_it6.931
r_mcangle_other6.929
r_scbond_it5.634
r_scbond_other5.632
r_mcbond_other5.109
r_mcbond_it5.108
r_angle_refined_deg1.765
r_angle_other_deg1.002
r_chiral_restr0.099
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3217
Nucleic Acid Atoms
Solvent Atoms7
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing