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Protein 19 with aldehyde deformylating oxidase activity from Synechococcus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UW2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 25.9 mg/ml 17% PEG 4000, 8.5 isopropanol, 85 mM Hepes
Crystal Properties Matthews coefficient Solvent content 2.39 48.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.986 α = 90 b = 90.227 β = 90 c = 109.06 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 PIXEL DECTRIS PILATUS3 S 6M 2016-02-13 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 1.99 109.06 95.3 0.057 11.9 3.8 33222
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 5UW2 1.99 109.06 31991 1024 94.12 0.21238 0.21106 0.2217 0.25355 0.2618 RANDOM 40.704
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] -1.61 -1.08 2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.473 r_dihedral_angle_4_deg 17.934 r_dihedral_angle_3_deg 16.007 r_long_range_B_refined 6.195 r_long_range_B_other 6.195 r_dihedral_angle_1_deg 5.008 r_scangle_other 4.797 r_mcangle_it 3.409 r_mcangle_other 3.408 r_scbond_it 3.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.473 r_dihedral_angle_4_deg 17.934 r_dihedral_angle_3_deg 16.007 r_long_range_B_refined 6.195 r_long_range_B_other 6.195 r_dihedral_angle_1_deg 5.008 r_scangle_other 4.797 r_mcangle_it 3.409 r_mcangle_other 3.408 r_scbond_it 3.057 r_scbond_other 3.056 r_mcbond_other 2.446 r_mcbond_it 2.445 r_angle_refined_deg 1.355 r_angle_other_deg 0.819 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 3438 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing