☰ Navigation Tabs
Crystal structure of 1,6-APD (2-ANIMOPHENOL-1,6-DIOXYGENASE) complexed with intermediate products
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 2.6 52.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 270.24 α = 90 b = 48.39 β = 109.57 c = 108.55 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 98 IMAGE PLATE RIGAKU RAXIS IV++ MIRRORS 2007-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 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 2.3 39.87 97.76 0.109 0.109 15.7 5.2 59609 55311 31
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 2.3 2.42 86.5 0.456 0.456 2.7 3.9
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 2.3 39.87 59609 55311 2947 97.76 0.192 0.19188 0.18962 0.191 0.23397 0.2348 RANDOM 20.072
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] -0.19 -0.91 0.32 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.903 r_dihedral_angle_3_deg 15.964 r_dihedral_angle_4_deg 14.524 r_dihedral_angle_1_deg 5.66 r_scangle_it 1.3 r_angle_refined_deg 1.033 r_angle_other_deg 0.828 r_scbond_it 0.752 r_mcangle_it 0.56 r_mcbond_it 0.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.903 r_dihedral_angle_3_deg 15.964 r_dihedral_angle_4_deg 14.524 r_dihedral_angle_1_deg 5.66 r_scangle_it 1.3 r_angle_refined_deg 1.033 r_angle_other_deg 0.828 r_scbond_it 0.752 r_mcangle_it 0.56 r_mcbond_it 0.291 r_chiral_restr 0.058 r_mcbond_other 0.038 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8892 Nucleic Acid Atoms Solvent Atoms 1035 Heterogen Atoms 23
Software Software Software Name Purpose CrystalClear data collection PHASES phasing REFMAC refinement MOSFLM data reduction SCALA data scaling