4PVF

Crystal structure of Homo sapiens holo serine hydroxymethyltransferase 2 (mitochondrial) (SHMT2), isoform 3, transcript variant 5, 483 aa, at 2.6 ang. resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OU5PDB ENTRY 3OU5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52940.1M Bis-Tris propane pH7.5, 5%glycerol, 12-16% Peg 3350, 0.2M KF, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.6566.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 160.462α = 90
b = 160.462β = 90
c = 211.461γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6MSagitally bended Si111-crystal2013-03-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9798BESSY14.1

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
12.6138.96410015.4499904999022
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.691001.815.84519

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3OU52.6138.964992649926253199.970.20770.20580.2435RANDOM34.6141
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]
0.460.230.46-1.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.152
r_dihedral_angle_4_deg21.794
r_dihedral_angle_3_deg18.639
r_dihedral_angle_1_deg6.516
r_mcangle_it4.329
r_mcbond_it2.737
r_mcbond_other2.737
r_angle_refined_deg1.747
r_angle_other_deg1.141
r_chiral_restr0.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.152
r_dihedral_angle_4_deg21.794
r_dihedral_angle_3_deg18.639
r_dihedral_angle_1_deg6.516
r_mcangle_it4.329
r_mcbond_it2.737
r_mcbond_other2.737
r_angle_refined_deg1.747
r_angle_other_deg1.141
r_chiral_restr0.087
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7073
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms19

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction