6S4A

Structure of human MTHFD2 in complex with TH9028


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M HEPES pH 7.8, 80 % v/v MPD
Crystal Properties
Matthews coefficientSolvent content
3.1661.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.068α = 90
b = 115.068β = 90
c = 113.549γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2016-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.00SLSX06SA

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
11.9549.399.913.510.262083
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.95113.5558965307399.890.170130.168110.21138RANDOM58.736
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]
1.740.871.74-5.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.08
r_dihedral_angle_4_deg20.031
r_dihedral_angle_3_deg13.677
r_long_range_B_refined10.194
r_long_range_B_other10.194
r_scangle_other8.222
r_dihedral_angle_1_deg6.082
r_scbond_it5.771
r_scbond_other5.77
r_mcangle_it5.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.08
r_dihedral_angle_4_deg20.031
r_dihedral_angle_3_deg13.677
r_long_range_B_refined10.194
r_long_range_B_other10.194
r_scangle_other8.222
r_dihedral_angle_1_deg6.082
r_scbond_it5.771
r_scbond_other5.77
r_mcangle_it5.106
r_mcangle_other5.105
r_mcbond_it3.818
r_mcbond_other3.816
r_angle_refined_deg1.809
r_angle_other_deg1
r_chiral_restr0.094
r_bond_refined_d0.014
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 Atoms4483
Nucleic Acid Atoms
Solvent Atoms229
Heterogen Atoms240

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing