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Crystal structures of aldehyde deformylating oxygenase from Oscillatoria sp. KNUA011
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QUW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296 Tris, Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2 38.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.012 α = 90 b = 78.265 β = 90 c = 108.861 γ = 90
Symmetry Space Group P 21 21 21
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 4 2015-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97953 PAL/PLS 7A (6B, 6C1)
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 1.8 50.01 97.4 0.077 12 7.7 43714
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 1.8 1.83 97.7 8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4QUW 1.8 50.01 41104 2096 97.41 0.1949 0.1929 0.2341 0.2399 RANDOM 41.613
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] 1.81 -0.56 -1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.245 r_dihedral_angle_4_deg 23.355 r_dihedral_angle_3_deg 15.889 r_dihedral_angle_1_deg 5.132 r_mcangle_it 3.987 r_mcbond_it 3.261 r_mcbond_other 3.252 r_angle_refined_deg 1.84 r_angle_other_deg 1.179 r_chiral_restr 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.245 r_dihedral_angle_4_deg 23.355 r_dihedral_angle_3_deg 15.889 r_dihedral_angle_1_deg 5.132 r_mcangle_it 3.987 r_mcbond_it 3.261 r_mcbond_other 3.252 r_angle_refined_deg 1.84 r_angle_other_deg 1.179 r_chiral_restr 0.124 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3456 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 42
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing