3CL9

Structure of bifunctional TcDHFR-TS in complex with MTX


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2H2Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629517% 2-METHYL-2,4-PENTANEDIOL, 10% PEG 4000, 0.1M POTASSIUM CITRATE, PH 6.0, , VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
4.0569.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.05α = 90
b = 121.05β = 90
c = 260.76γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID0.9998APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
13.319.7897.50.010.019.65.11455514555187
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.33.4299.50.4333.25.31601

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 (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2H2Q3.319.78138091380973897.470.208330.206260.24901RANDOM90.8
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]
0.030.03-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.899
r_dihedral_angle_3_deg20.152
r_dihedral_angle_4_deg15.737
r_dihedral_angle_1_deg5.899
r_scangle_it1.466
r_angle_refined_deg1.322
r_scbond_it0.811
r_mcangle_it0.774
r_mcbond_it0.428
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.899
r_dihedral_angle_3_deg20.152
r_dihedral_angle_4_deg15.737
r_dihedral_angle_1_deg5.899
r_scangle_it1.466
r_angle_refined_deg1.322
r_scbond_it0.811
r_mcangle_it0.774
r_mcbond_it0.428
r_nbtor_refined0.313
r_nbd_refined0.222
r_symmetry_hbond_refined0.207
r_symmetry_vdw_refined0.176
r_xyhbond_nbd_refined0.148
r_chiral_restr0.085
r_bond_refined_d0.01
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4015
Nucleic Acid Atoms
Solvent Atoms20
Heterogen Atoms122

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing