5TC4

Crystal structure of human mitochondrial methylenetetrahydrofolate dehydrogenase-cyclohydrolase (MTHFD2) in complex with LY345899 and cofactors


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1B0A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M Phosphate/Citrate pH 4.1, 38 % v/v PEG300, in presence of 1:50 ratio each of trypsin, alpha-chymotrypsin, pepsin, papain, proteinase K and subtilisin to MTHFD2
Crystal Properties
Matthews coefficientSolvent content
1.9838.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.323α = 90
b = 74.323β = 90
c = 98.62γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-09-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.9677ESRFMASSIF-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.8937.1699.80.3160.986.86.921322
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.891.9396.84.3480.2970.96.7

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 REPLACEMENTTHROUGHOUT1B0A1.8937.1620245107399.760.165090.16260.21222RANDOM28.27
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]
0.040.04-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.827
r_dihedral_angle_4_deg20.267
r_dihedral_angle_3_deg15.236
r_long_range_B_refined6.253
r_long_range_B_other6.066
r_dihedral_angle_1_deg6.042
r_scangle_other2.602
r_angle_refined_deg2.276
r_scbond_it1.642
r_scbond_other1.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.827
r_dihedral_angle_4_deg20.267
r_dihedral_angle_3_deg15.236
r_long_range_B_refined6.253
r_long_range_B_other6.066
r_dihedral_angle_1_deg6.042
r_scangle_other2.602
r_angle_refined_deg2.276
r_scbond_it1.642
r_scbond_other1.64
r_mcangle_other1.431
r_mcangle_it1.43
r_angle_other_deg1.17
r_mcbond_it0.901
r_mcbond_other0.897
r_chiral_restr0.137
r_bond_refined_d0.023
r_gen_planes_refined0.011
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 Atoms2216
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms83

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing