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Crystal Structure of Holo-ACP-synthase from Plasmodium yoelii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F80 PDB ENTRY 1F80
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 297 16% PEG8000, 0.2M Mg acetate, 0.1M Na Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.64 53.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.771 α = 90 b = 86.771 β = 90 c = 86.771 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV VeriMax HR 2005-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.28 28.9 100 0.099 0.099 6.9 14.2 10191 10191 41.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.32 100 0.936 0.936 2.8 14.3 493
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1F80 2.28 28.9 9689 9689 485 99.95 0.2027 0.2027 0.20028 0.2021 0.25146 0.1917 RANDOM 40.254
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.253 r_dihedral_angle_3_deg 16.895 r_dihedral_angle_4_deg 14.544 r_dihedral_angle_1_deg 7.359 r_scangle_it 4.748 r_scbond_it 3.138 r_mcangle_it 2.494 r_angle_refined_deg 1.792 r_mcbond_it 1.516 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.253 r_dihedral_angle_3_deg 16.895 r_dihedral_angle_4_deg 14.544 r_dihedral_angle_1_deg 7.359 r_scangle_it 4.748 r_scbond_it 3.138 r_mcangle_it 2.494 r_angle_refined_deg 1.792 r_mcbond_it 1.516 r_nbtor_refined 0.306 r_nbd_refined 0.219 r_symmetry_hbond_refined 0.205 r_xyhbond_nbd_refined 0.203 r_symmetry_vdw_refined 0.15 r_chiral_restr 0.139 r_bond_refined_d 0.024 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 1014 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data scaling PHASER phasing Coot model building