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Plasmodium falciparum Atg8 in complex with Plasmodium falciparum Atg3 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other 20 models (15 PDB 5 predicted) as ensemble using phenix.automr
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 0.1 M MES pH 6.5, 0.1 M Ca(OAc)2, 20% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.2 44.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.3 α = 90 b = 111.08 β = 92.58 c = 57.09 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 PSI PILATUS 6M 2012-02-20 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2012-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.0332 SSRL BL12-2 2 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
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 1,2 2.22 31.06 83.4 0.215 7.28 2.07 21538 17965 20402 -3 29.081
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 2.18 2.24 45 0.918 1.6 2.18 1605
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 20 models (15 PDB 5 predicted) as ensemble using phenix.automr 2.22 20 -3 21538 14961 801 77.37 0.20839 0.20463 0.2124 0.27965 0.2774 RANDOM 39.76
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] -10.8 -8.64 -9.05 19.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.72 r_dihedral_angle_3_deg 14.544 r_dihedral_angle_4_deg 14.175 r_dihedral_angle_1_deg 5.771 r_angle_refined_deg 1.197 r_angle_other_deg 1.141 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.72 r_dihedral_angle_3_deg 14.544 r_dihedral_angle_4_deg 14.175 r_dihedral_angle_1_deg 5.771 r_angle_refined_deg 1.197 r_angle_other_deg 1.141 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 3289 Nucleic Acid Atoms Solvent Atoms 331 Heterogen Atoms 23
Software Software Software Name Purpose Blu-Ice data collection PHENIX model building REFMAC refinement XDS data reduction XSCALE data scaling PHENIX phasing