3I3R

X-ray structure dihydrofolate reductase/thymidylate synthase from babesia bovis at 2.35A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QZFpdb entry 1QZF modified by the ccp4 program chainsaw

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROFLUDIC MICROBATCH IN A CRYSTAL CARD9.5290WIZARD SCREEN A1: 20% PEG 8000, 100MM CHES PH 9.5; BABOA.01191.A AT 11.3MG/ML, MICROFLUDIC MICROBATCH IN A CRYSTAL CARD, TEMPERATURE 290K
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.54α = 119
b = 83.48β = 97.99
c = 84.19γ = 100.69
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0000ALS5.0.2

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
12.3572.296.80.0999.642.94799547995-3-336.4
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)
12.352.4196.70.5512.22.9

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1QZF modified by the ccp4 program chainsaw2.3519.694799547995244097.20.2050.2020.251RANDOM23.29
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]
-0.051.040.341.261.40.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.08
r_dihedral_angle_4_deg21.604
r_dihedral_angle_3_deg14.502
r_dihedral_angle_1_deg6.815
r_scangle_it2.056
r_scbond_it1.26
r_angle_refined_deg1.191
r_mcangle_it0.938
r_angle_other_deg0.843
r_mcbond_it0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.08
r_dihedral_angle_4_deg21.604
r_dihedral_angle_3_deg14.502
r_dihedral_angle_1_deg6.815
r_scangle_it2.056
r_scbond_it1.26
r_angle_refined_deg1.191
r_mcangle_it0.938
r_angle_other_deg0.843
r_mcbond_it0.5
r_mcbond_other0.092
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7607
Nucleic Acid Atoms
Solvent Atoms253
Heterogen Atoms2

Software

Software
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling