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Crystal structure of dihydrofolate reductase/thymidylate synthase from Babesia bovis determined using SlipChip based microfluidics
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I3R PDBid:3I3R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SlipChip based Microbatch 9.5 296 a 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 coefficient Solvent content 2.66 53.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.113 α = 90 b = 97.559 β = 90 c = 152.83 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2009-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.95 50 98.2 0.073 14 2.8 163926 89311
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 98.4 0.47 2.1 2.6 7863
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDBid:3I3R 1.95 50 84792 4477 98.1 0.17025 0.16863 0.1685 0.20112 0.2012 RANDOM 18.604
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 -0.15 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.511 r_dihedral_angle_4_deg 14.994 r_dihedral_angle_3_deg 13.244 r_dihedral_angle_1_deg 6.257 r_scangle_it 2.931 r_scbond_it 1.829 r_angle_refined_deg 1.356 r_mcangle_it 1.175 r_mcbond_it 0.644 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.511 r_dihedral_angle_4_deg 14.994 r_dihedral_angle_3_deg 13.244 r_dihedral_angle_1_deg 6.257 r_scangle_it 2.931 r_scbond_it 1.829 r_angle_refined_deg 1.356 r_mcangle_it 1.175 r_mcbond_it 0.644 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 Atoms Number Protein Atoms 7876 Nucleic Acid Atoms Solvent Atoms 891 Heterogen Atoms 139
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling