3CLB

Structure of bifunctional TcDHFR-TS in complex with TMQ


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629517% MPD, 10% PEG 4000, 0.1M Potassium citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
4.1770.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 176.571α = 90
b = 176.571β = 90
c = 251.848γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
1324.9797.20.1527.96.77764377643154
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)
133.1198.30.47236.87755

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-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2H2Q319.947356873568389897.140.20930.20930.207470.24489RANDOM57.26
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]
0.240.24-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.953
r_dihedral_angle_3_deg17.79
r_dihedral_angle_4_deg17.616
r_dihedral_angle_1_deg5.378
r_scangle_it1.244
r_angle_refined_deg1.162
r_scbond_it0.701
r_mcangle_it0.666
r_mcbond_it0.368
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.953
r_dihedral_angle_3_deg17.79
r_dihedral_angle_4_deg17.616
r_dihedral_angle_1_deg5.378
r_scangle_it1.244
r_angle_refined_deg1.162
r_scbond_it0.701
r_mcangle_it0.666
r_mcbond_it0.368
r_nbtor_refined0.307
r_nbd_refined0.195
r_symmetry_vdw_refined0.177
r_xyhbond_nbd_refined0.121
r_symmetry_hbond_refined0.09
r_chiral_restr0.075
r_bond_refined_d0.008
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 Atoms16180
Nucleic Acid Atoms
Solvent Atoms94
Heterogen Atoms344

Software

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