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Structure of full-length peroxisomal multifunctional enzyme type 2 from Drosophila melanogaster
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PN4 PDB ENTRIES 1PN4 AND 1GZ6 experimental model PDB 1GZ6 PDB ENTRIES 1PN4 AND 1GZ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 294 0.1 M Tris, 1.0 M NaCl, 20 % (w/v) PEG 5000 MME, 5 mM NAD+ , VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.21 44.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.48 α = 90 b = 114.48 β = 90 c = 89.11 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2008-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9310 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.15 28.1 99.66 31114 31008
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.21 99.7
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 (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 ENTRIES 1PN4 AND 1GZ6 2.15 28.1 31114 31008 1636 99.66 0.23686 0.23431 0.235 0.28542 0.2842 RANDOM 65.23
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] 0.15 0.15 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.611 r_dihedral_angle_4_deg 17.756 r_dihedral_angle_3_deg 15.866 r_dihedral_angle_1_deg 5.939 r_scangle_it 1.981 r_scbond_it 1.315 r_angle_refined_deg 1.202 r_mcangle_it 0.812 r_mcbond_it 0.447 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.611 r_dihedral_angle_4_deg 17.756 r_dihedral_angle_3_deg 15.866 r_dihedral_angle_1_deg 5.939 r_scangle_it 1.981 r_scbond_it 1.315 r_angle_refined_deg 1.202 r_mcangle_it 0.812 r_mcbond_it 0.447 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4038 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling