7TH5

Thermus thermophilus methylenetetrahydrofolate reductase


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52970.1M Tris-HCl pH 8.5, 3M NaCl
Crystal Properties
Matthews coefficientSolvent content
2.7254.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.496α = 90
b = 91.288β = 90
c = 130.261γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-06-28MSINGLE 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
12.0947.0798.70.1180.1380.0690.9937.63.942742
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)
12.092.1588.40.6210.6210.3160.6743.5

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 REPLACEMENTTHROUGHOUT3APY2.0947.0740515215798.680.18380.18170.2239RANDOM34.665
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]
0.851.27-2.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.433
r_dihedral_angle_4_deg23.427
r_dihedral_angle_3_deg16.06
r_dihedral_angle_1_deg6.225
r_angle_refined_deg1.618
r_angle_other_deg0.532
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.433
r_dihedral_angle_4_deg23.427
r_dihedral_angle_3_deg16.06
r_dihedral_angle_1_deg6.225
r_angle_refined_deg1.618
r_angle_other_deg0.532
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4547
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms160

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing