7TH4

T. thermophilus methylenetetrahydrofolate reductase complex with 5-formyltetrahydrofolate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3APY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52770.1M sodium acetate buffer pH 4.5, 2.5M NaCl, 0.2M lithium sulfate, 1.2% myo-inositol
Crystal Properties
Matthews coefficientSolvent content
2.4650.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.069α = 90
b = 89.545β = 90
c = 161.258γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-03-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0332APS23-ID-D

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
11.4546.1399.70.0860.0980.0460.99510.74.3116419
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)
11.451.4799.30.9790.11440.5810.6743.7

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 REPLACEMENTTHROUGHOUT3APY1.4546.13110406591599.830.13350.13110.1783RANDOM32.344
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]
-0.220.52-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.522
r_dihedral_angle_4_deg17.121
r_dihedral_angle_3_deg13.08
r_rigid_bond_restr7.332
r_dihedral_angle_1_deg5.929
r_angle_refined_deg1.587
r_angle_other_deg0.56
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.522
r_dihedral_angle_4_deg17.121
r_dihedral_angle_3_deg13.08
r_rigid_bond_restr7.332
r_dihedral_angle_1_deg5.929
r_angle_refined_deg1.587
r_angle_other_deg0.56
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4596
Nucleic Acid Atoms
Solvent Atoms445
Heterogen Atoms288

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing