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Crystal structure of glutathione-dependent phospholipid peroxidase Hyr1 from the yeast Saccharomyces cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P5Q PDB ENTRY 2P5Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 289 0.2M Ammonium Acetate, 0.1M Sodium Acetate trihydrate, pH4.6, 30% polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.35 47.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.57 α = 90 b = 64.88 β = 90 c = 72.02 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 IMAGE PLATE MAR scanner 345 mm plate 2007-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 39.56 93.9 0.057 0.064 4.8 12069 2 30.674
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 2.11 81.5 0.336 0.376 3.6 4.5 1518
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 2P5Q 2.02 34.68 3 8294 418 68.58 0.22597 0.22438 0.2239 0.25602 0.2598 RANDOM 37.304
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] 1.81 1.46 -3.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.632 r_dihedral_angle_4_deg 18.101 r_dihedral_angle_3_deg 16.379 r_dihedral_angle_1_deg 5.271 r_scangle_it 1.234 r_angle_refined_deg 1.168 r_scbond_it 0.836 r_mcangle_it 0.47 r_nbtor_refined 0.305 r_mcbond_it 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.632 r_dihedral_angle_4_deg 18.101 r_dihedral_angle_3_deg 16.379 r_dihedral_angle_1_deg 5.271 r_scangle_it 1.234 r_angle_refined_deg 1.168 r_scbond_it 0.836 r_mcangle_it 0.47 r_nbtor_refined 0.305 r_mcbond_it 0.294 r_symmetry_hbond_refined 0.24 r_symmetry_vdw_refined 0.196 r_nbd_refined 0.179 r_xyhbond_nbd_refined 0.106 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 1150 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection MOSFLM data reduction SCALA data scaling MOLREP phasing