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Crystal structure of cyanobacterial aldehyde-deformylating oxygenase bound with fatty acid
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, SITTING DROP 7.1 291 0.2M L-proline, 0.1M Hepes pH 7.1, 25%(w/v) PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.35 47.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.628 α = 90 b = 61.984 β = 90 c = 124.781 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 315r 2013-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.71 50 99.8 52391 52286
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 1.71 1.74 100
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 (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 4QUW 1.71 43.703 49687 49558 2663 99.74 0.189 0.189 0.1905 0.212 0.1935 RANDOM 15.333
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] -0.11 -0.1 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.686 r_dihedral_angle_4_deg 15.716 r_dihedral_angle_3_deg 12.555 r_long_range_B_refined 5.007 r_long_range_B_other 4.512 r_dihedral_angle_1_deg 3.965 r_angle_other_deg 3.603 r_scangle_other 2.43 r_scbond_it 1.617 r_scbond_other 1.616
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.686 r_dihedral_angle_4_deg 15.716 r_dihedral_angle_3_deg 12.555 r_long_range_B_refined 5.007 r_long_range_B_other 4.512 r_dihedral_angle_1_deg 3.965 r_angle_other_deg 3.603 r_scangle_other 2.43 r_scbond_it 1.617 r_scbond_other 1.616 r_angle_refined_deg 1.018 r_mcangle_it 0.969 r_mcangle_other 0.969 r_mcbond_it 0.582 r_mcbond_other 0.577 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_other 0.004 r_gen_planes_refined 0.003 r_bond_other_d 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 3560 Nucleic Acid Atoms Solvent Atoms 605 Heterogen Atoms 22
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling