6FL5

Structure of human SHMT1-H135N-R137A-E168N mutant at 3.6 Ang. resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BJ4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52942 microL of 80microM protein solution in: 20 mM Hepes pH7.2, 250 mM NaCl 5% glycerol + 2 microL of reservoir:0.1 M Na Cacodilate pH6.5 - 1M Na citrate
Crystal Properties
Matthews coefficientSolvent content
3.1761.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.719α = 90
b = 139.719β = 90
c = 267.377γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER R 4MCRL2017-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.96770ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
13.656.6198.20.3120.340.1310.9735.66.330938
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.63.7999.21.0191.1070.4250.576.5

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 REPLACEMENTTHROUGHOUT1BJ43.650.0129318154598.020.2630.26220.2771RANDOM74.364
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]
2.932.93-5.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.068
r_dihedral_angle_4_deg12.658
r_dihedral_angle_3_deg12.18
r_dihedral_angle_1_deg3.553
r_angle_refined_deg0.638
r_angle_other_deg0.508
r_chiral_restr0.035
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_bond_other_d
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.068
r_dihedral_angle_4_deg12.658
r_dihedral_angle_3_deg12.18
r_dihedral_angle_1_deg3.553
r_angle_refined_deg0.638
r_angle_other_deg0.508
r_chiral_restr0.035
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_bond_other_d
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14328
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction