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Crystal structure of truncated unliganded Aspartate Transcarbamoylase from Plasmodium falciparum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ML4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 200 mM Sodium Sulphate, 5 mM MgSO4, 15-18 % (w/v) PEG 3350 in 100mM bis-Tris Propane pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.98 α = 90 b = 103.8 β = 117.68 c = 87.11 γ = 90
Symmetry Space Group P 1 21 1
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 2014-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.42 45.03 95.2 0.062 0.076 0.997 10.81 2.51 45217 56.64
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 2.42 2.56 95.6 0.58 1.98
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 FREE R-VALUE 1ML4 2.5 45.03 45217 2136 95.1 0.2082 0.2083 0.2107 0.2502 0.2547 RANDOM 65.6806
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] 0.02 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.178 r_dihedral_angle_4_deg 22.989 r_dihedral_angle_3_deg 17.218 r_dihedral_angle_1_deg 7.341 r_mcangle_it 4.464 r_angle_other_deg 3.787 r_mcbond_it 2.821 r_mcbond_other 2.821 r_angle_refined_deg 1.961 r_chiral_restr 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.178 r_dihedral_angle_4_deg 22.989 r_dihedral_angle_3_deg 17.218 r_dihedral_angle_1_deg 7.341 r_mcangle_it 4.464 r_angle_other_deg 3.787 r_mcbond_it 2.821 r_mcbond_other 2.821 r_angle_refined_deg 1.961 r_chiral_restr 0.117 r_bond_refined_d 0.019 r_gen_planes_other 0.016 r_gen_planes_refined 0.009 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7798 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Coot model building XDS data reduction Aimless data scaling MOLREP phasing