3KJR

Crystal structure of dihydrofolate reductase/thymidylate synthase from Babesia bovis determined using SlipChip based microfluidics


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3I3RPDBid:3I3R

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SlipChip based Microbatch9.5296a protein sample was mixed at 1:2 ratio with 20 % (w/v) PEG-8000, 0.2 M NaCl and 0.1 M CHES, pH 9.5, SlipChip based Microbatch, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.6653.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.113α = 90
b = 97.559β = 90
c = 152.83γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2009-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.0332APS23-ID-B

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
11.955098.20.073142.816392689311
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)
11.951.9898.40.472.12.67863

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 REPLACEMENTTHROUGHOUTPDBid:3I3R1.955084792447798.10.170250.168630.20112RANDOM18.604
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]
-0.76-0.150.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.511
r_dihedral_angle_4_deg14.994
r_dihedral_angle_3_deg13.244
r_dihedral_angle_1_deg6.257
r_scangle_it2.931
r_scbond_it1.829
r_angle_refined_deg1.356
r_mcangle_it1.175
r_mcbond_it0.644
r_chiral_restr0.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.511
r_dihedral_angle_4_deg14.994
r_dihedral_angle_3_deg13.244
r_dihedral_angle_1_deg6.257
r_scangle_it2.931
r_scbond_it1.829
r_angle_refined_deg1.356
r_mcangle_it1.175
r_mcbond_it0.644
r_chiral_restr0.097
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7876
Nucleic Acid Atoms
Solvent Atoms891
Heterogen Atoms139

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling