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Structure of the apo form of AioX from Rhizobium sp. str. NT-26
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ESV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 20% PEG 3350, 0.2 M sodium malonate and 0.1 M Bis-Tris propane, pH 8.5
Crystal Properties Matthews coefficient Solvent content 3.15 61.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.877 α = 90 b = 124.877 β = 90 c = 47.734 γ = 90
Symmetry Space Group P 43 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 PILATUS 6M-F 2015-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.987 Diamond I02
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 1.75 44.59 98.9 7.6 12.8 38474
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 6ESV 1.75 88.3 36519 1864 98.95 0.18854 0.18737 0.1987 0.21115 0.2226 RANDOM 29.719
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.681 r_dihedral_angle_4_deg 18.691 r_dihedral_angle_3_deg 13.839 r_long_range_B_refined 8.98 r_long_range_B_other 8.978 r_scangle_other 7.412 r_dihedral_angle_1_deg 6.166 r_scbond_it 4.812 r_scbond_other 4.811 r_mcangle_other 4.052
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.681 r_dihedral_angle_4_deg 18.691 r_dihedral_angle_3_deg 13.839 r_long_range_B_refined 8.98 r_long_range_B_other 8.978 r_scangle_other 7.412 r_dihedral_angle_1_deg 6.166 r_scbond_it 4.812 r_scbond_other 4.811 r_mcangle_other 4.052 r_mcangle_it 4.046 r_mcbond_it 2.93 r_mcbond_other 2.886 r_angle_refined_deg 1.969 r_angle_other_deg 1.088 r_chiral_restr 0.133 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.006 r_gen_planes_other 0.002 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 2068 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing