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Crystal structure of native 1,6-APD (with Iron), 2-Animophenol-1,6-Dioxygenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VSG PDB ENTRY 3VSG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 25% PEG 3350, 0.2M SODIUM CHLORIDE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.48 50.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 265.39 α = 90 b = 47.47 β = 109.47 c = 107.38 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 210 2007-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 2.7 47.95 98.1 0.119 0.119 11.5 3.2 35399 34673 47
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 2.7 2.85 93.7 0.333 0.333 2.7 2.6
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 3VSG 2.7 47.93 35399 32952 1719 98 0.178 0.178 0.175 0.1755 0.247 0.2458 RANDOM 32.23
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] -1.55 -1.28 2.28 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.401 r_dihedral_angle_3_deg 18.176 r_dihedral_angle_4_deg 15.313 r_dihedral_angle_1_deg 5.466 r_angle_refined_deg 1.118 r_chiral_restr 0.071 r_gen_planes_refined 0.012 r_bond_refined_d 0.007 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.401 r_dihedral_angle_3_deg 18.176 r_dihedral_angle_4_deg 15.313 r_dihedral_angle_1_deg 5.466 r_angle_refined_deg 1.118 r_chiral_restr 0.071 r_gen_planes_refined 0.012 r_bond_refined_d 0.007 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_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 8915 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms 2
Software Software Software Name Purpose ADSC data collection PHASES phasing REFMAC refinement MOSFLM data reduction SCALA data scaling