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Protein 84 with aldehyde deformylating oxygenase activity from Sulfolobus tokodaii (monoclinic)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other theoretical
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 Potassium phosphate, PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.54 51.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.536 α = 90 b = 64.849 β = 116.86 c = 71.299 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 100 PIXEL DECTRIS PILATUS3 6M 2016-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
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 1.72 63.61 96.5 0.05 20.2 6.7 55207
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 1.72 1.75 57 0.251 3.7
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 theoretical 1.72 63.61 51501 1647 96.23 0.1961 0.1952 0.2058 0.22341 0.2294 RANDOM 22.536
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] 1.21 0.26 -0.29 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.641 r_dihedral_angle_4_deg 15.556 r_dihedral_angle_3_deg 14.977 r_long_range_B_refined 6.116 r_long_range_B_other 6.069 r_scangle_other 4.925 r_dihedral_angle_1_deg 4.798 r_scbond_it 3.125 r_scbond_other 3.123 r_mcangle_other 2.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.641 r_dihedral_angle_4_deg 15.556 r_dihedral_angle_3_deg 14.977 r_long_range_B_refined 6.116 r_long_range_B_other 6.069 r_scangle_other 4.925 r_dihedral_angle_1_deg 4.798 r_scbond_it 3.125 r_scbond_other 3.123 r_mcangle_other 2.634 r_mcangle_it 2.633 r_mcbond_it 1.829 r_mcbond_other 1.809 r_angle_refined_deg 1.76 r_angle_other_deg 0.86 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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 3515 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing