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Structure of the 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 294 0.1 M sodium cacodylate pH 5.9 - 6.8.
1.1 - 1.6 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.82 56.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.25 α = 90 b = 83.25 β = 90 c = 114.28 γ = 120
Symmetry Space Group P 65 2 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 PIXEL DECTRIS PILATUS 2M 2014-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.920 Diamond I04-1
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 1.88 41.62 99.5 0.122 21.8 20.3 19556
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 1.88 1.93 99 0.8 5 19.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4p9g 1.88 41.62 18593 938 99.31 0.14345 0.14195 0.146 0.1718 0.1734 RANDOM 25.147
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] 0.26 0.13 0.26 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.98 r_dihedral_angle_4_deg 19.292 r_dihedral_angle_3_deg 14.476 r_long_range_B_refined 10.32 r_long_range_B_other 10.191 r_scangle_other 8.315 r_dihedral_angle_1_deg 6.821 r_scbond_it 5.432 r_scbond_other 5.428 r_mcangle_it 3.703
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.98 r_dihedral_angle_4_deg 19.292 r_dihedral_angle_3_deg 14.476 r_long_range_B_refined 10.32 r_long_range_B_other 10.191 r_scangle_other 8.315 r_dihedral_angle_1_deg 6.821 r_scbond_it 5.432 r_scbond_other 5.428 r_mcangle_it 3.703 r_mcangle_other 3.702 r_mcbond_it 2.54 r_mcbond_other 2.531 r_angle_refined_deg 2.233 r_angle_other_deg 1.803 r_chiral_restr 0.175 r_bond_refined_d 0.025 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1257 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling