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Protein 84 with aldehyde deformylating oxygenase activity from Sulfolobus tokodaii (orthorhombic form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UXG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 10% ethanol, 1.5 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.56 51.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.466 α = 90 b = 114.36 β = 90 c = 64.857 γ = 90
Symmetry Space Group P 21 21 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 PILATUS3 S 6M 2016-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979460 SSRL BL9-2
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 1.7 38.12 99.7 18.5 5.9 59271
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 5UXG 1.7 38.12 57262 1752 99.53 0.18978 0.18888 0.2004 0.21963 0.223 RANDOM 22.553
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] -0.33 1.11 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.167 r_dihedral_angle_4_deg 18.376 r_dihedral_angle_3_deg 13.018 r_long_range_B_refined 6.075 r_long_range_B_other 6.075 r_scangle_other 5.04 r_dihedral_angle_1_deg 4.853 r_scbond_it 3.343 r_scbond_other 3.343 r_mcangle_other 2.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.167 r_dihedral_angle_4_deg 18.376 r_dihedral_angle_3_deg 13.018 r_long_range_B_refined 6.075 r_long_range_B_other 6.075 r_scangle_other 5.04 r_dihedral_angle_1_deg 4.853 r_scbond_it 3.343 r_scbond_other 3.343 r_mcangle_other 2.9 r_mcangle_it 2.899 r_mcbond_it 1.967 r_mcbond_other 1.957 r_angle_refined_deg 1.726 r_angle_other_deg 0.906 r_chiral_restr 0.119 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 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 3522 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing