6QVG

Human SHMT2 in complex with lometrexol


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2910.1 M Bis-tris pH 6.5, 28 % PEGMME2000
Crystal Properties
Matthews coefficientSolvent content
3.3863.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 158.807α = 90
b = 158.807β = 90
c = 208.257γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I041.07DiamondI04

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
12.32208.399.814.739.32640873
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32208.3

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 REPLACEMENTTHROUGHOUT2.32208.2663841336999.730.201120.19930.2358RANDOM37.101
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]
0.510.260.51-1.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.166
r_dihedral_angle_4_deg18.166
r_dihedral_angle_3_deg15.646
r_dihedral_angle_1_deg6.457
r_long_range_B_refined5.303
r_long_range_B_other5.303
r_scangle_other3.079
r_mcangle_it2.817
r_mcangle_other2.817
r_scbond_it1.781
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.166
r_dihedral_angle_4_deg18.166
r_dihedral_angle_3_deg15.646
r_dihedral_angle_1_deg6.457
r_long_range_B_refined5.303
r_long_range_B_other5.303
r_scangle_other3.079
r_mcangle_it2.817
r_mcangle_other2.817
r_scbond_it1.781
r_scbond_other1.78
r_mcbond_it1.676
r_mcbond_other1.675
r_angle_refined_deg1.43
r_angle_other_deg0.965
r_chiral_restr0.08
r_bond_refined_d0.009
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 Atoms7087
Nucleic Acid Atoms
Solvent Atoms368
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing