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Crystal structure of CabE, an aromatic hydroxylase from angucycline biosynthesis, determined to 2.7 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QA1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 20 % PEG 3350, 0.1M bis-tris propane, 0.2M Na/K-phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.98 69.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.1 α = 90 b = 133.1 β = 90 c = 166.8 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 CCD MAR CCD 165 mm 2006-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 30 99.1 0.097 0.097 16.22 6.8 24379 24379 50.7
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 2.8 99.9 0.518 0.518 4 6.9 2467
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 2QA1 2.7 29.83 23190 23190 1220 99.4 0.23633 0.23633 0.23428 0.23 0.27428 0.2699 RANDOM 72.281
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] -2.71 -1.35 -2.71 4.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.661 r_dihedral_angle_3_deg 20.136 r_dihedral_angle_4_deg 18.525 r_dihedral_angle_1_deg 6.596 r_scangle_it 1.607 r_angle_refined_deg 1.403 r_mcangle_it 1.321 r_scbond_it 1.034 r_mcbond_it 0.768 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.661 r_dihedral_angle_3_deg 20.136 r_dihedral_angle_4_deg 18.525 r_dihedral_angle_1_deg 6.596 r_scangle_it 1.607 r_angle_refined_deg 1.403 r_mcangle_it 1.321 r_scbond_it 1.034 r_mcbond_it 0.768 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.238 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.155 r_chiral_restr 0.09 r_bond_refined_d 0.012 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 3675 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 53
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling