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Structure of the malonate-bound form of ArrX from Chrysiogenes arsenatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6X6B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 293 0.1 M sodium malonate pH 6.7, 18% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.406 α = 90 b = 55.602 β = 90 c = 91.44 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 EIGER X 16M 2019-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95372 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.68 47.51 99.8 0.999 15.6 6.7 31216
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.71 0.9
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6X6B 1.68 47.508 29630 1529 99.734 0.172 0.1704 0.2007 0.2079 21.632
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] -1.178 1.624 -0.446
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.01 r_dihedral_angle_4_deg 12.681 r_dihedral_angle_3_deg 12.112 r_dihedral_angle_1_deg 5.806 r_lrange_it 5.148 r_lrange_other 4.839 r_scangle_it 2.816 r_scangle_other 2.815 r_scbond_it 1.77 r_scbond_other 1.769
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.01 r_dihedral_angle_4_deg 12.681 r_dihedral_angle_3_deg 12.112 r_dihedral_angle_1_deg 5.806 r_lrange_it 5.148 r_lrange_other 4.839 r_scangle_it 2.816 r_scangle_other 2.815 r_scbond_it 1.77 r_scbond_other 1.769 r_mcangle_it 1.745 r_mcangle_other 1.745 r_angle_other_deg 1.302 r_angle_refined_deg 1.27 r_mcbond_it 1.064 r_mcbond_other 1.061 r_xyhbond_nbd_refined 0.257 r_nbd_other 0.201 r_symmetry_xyhbond_nbd_refined 0.197 r_nbd_refined 0.193 r_symmetry_nbd_other 0.171 r_nbtor_refined 0.163 r_symmetry_nbd_refined 0.153 r_symmetry_nbtor_other 0.092 r_chiral_restr 0.066 r_symmetry_xyhbond_nbd_other 0.02 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2030 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing