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Crystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with bound inhibitor 2,3-naphthalenediol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ILQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 100 mM Bis-tris propane pH 7.5
200 mM Na-sulphate
15 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.48 50.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.757 α = 90 b = 86.757 β = 90 c = 138.151 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2014-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.979 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 2 75.14 98.7 0.081 0.998 11.46 3.16 228939 74373 1.45
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.17 98.5 0.988 0.506 1.45 3.185
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5ILQ 2 75.13 74373 3991 99.69 0.18621 0.18417 0.22526 0.2141 RANDOM 43.799
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] 0.52 0.26 0.52 -1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.228 r_dihedral_angle_4_deg 25.49 r_dihedral_angle_3_deg 18.357 r_dihedral_angle_1_deg 6.632 r_long_range_B_refined 6.396 r_long_range_B_other 6.395 r_scangle_other 3.901 r_mcangle_it 2.996 r_mcangle_other 2.996 r_scbond_it 2.618
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.228 r_dihedral_angle_4_deg 25.49 r_dihedral_angle_3_deg 18.357 r_dihedral_angle_1_deg 6.632 r_long_range_B_refined 6.396 r_long_range_B_other 6.395 r_scangle_other 3.901 r_mcangle_it 2.996 r_mcangle_other 2.996 r_scbond_it 2.618 r_scbond_other 2.608 r_angle_refined_deg 2.307 r_mcbond_it 1.932 r_mcbond_other 1.93 r_angle_other_deg 1.217 r_chiral_restr 0.14 r_bond_refined_d 0.025 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7826 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction DIMPLE model building