5V7I

Crystal structure of homo sapiens serine hydroxymethyltransferase 2 (mitochondrial) (SHMT2), in complex with glycine, PLP and folate-competitive pyrazolopyran inhibitor: 6-amino-4-isopropyl-3-methyl-4-(3-(pyrrolidin-1-yl)-5-(trifluoromethyl)phenyl)-1,4-dihydropyrano[2,3-c]pyrazole-5-carbonitrile


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4PVF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52770.1 M TRIS ph 8.5, 17% (w/v) PEG 20000
Crystal Properties
Matthews coefficientSolvent content
3.6666.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 160.14α = 90
b = 160.14β = 90
c = 210.1γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2015-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.4783.7410018.0410.9157441

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 REPLACEMENTTHROUGHOUT4PVF2.478052776277596.70.2040.202260.23752RANDOM51.733
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]
1.320.661.32-4.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.85
r_dihedral_angle_4_deg13.952
r_dihedral_angle_3_deg13.184
r_long_range_B_refined6.218
r_long_range_B_other6.218
r_dihedral_angle_1_deg5.871
r_mcangle_other3.266
r_mcangle_it3.265
r_scangle_other2.922
r_mcbond_other1.874
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.85
r_dihedral_angle_4_deg13.952
r_dihedral_angle_3_deg13.184
r_long_range_B_refined6.218
r_long_range_B_other6.218
r_dihedral_angle_1_deg5.871
r_mcangle_other3.266
r_mcangle_it3.265
r_scangle_other2.922
r_mcbond_other1.874
r_mcbond_it1.873
r_scbond_it1.621
r_scbond_other1.62
r_angle_refined_deg1.238
r_angle_other_deg0.889
r_chiral_restr0.063
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
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 Atoms7246
Nucleic Acid Atoms
Solvent Atoms466
Heterogen Atoms93

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata processing
PHASERphasing
Cootmodel building