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High resolution structure of RgNanOx
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Z3B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG3000, sodium citrate,
Crystal Properties Matthews coefficient Solvent content 2.18 43.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.11 α = 90 b = 54.97 β = 90 c = 282.43 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 80 PIXEL DECTRIS PILATUS3 6M 2019-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 1.74 47.47 100 1 5.6 6.3 93221
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 1.74 1.77 0.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6Z3B 1.74 47.47 78180 3831 99.819 0.184 0.1821 0.1956 0.2226 0.2342 17.448
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] 0.996 -0.985 -0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.245 r_dihedral_angle_4_deg 23.814 r_dihedral_angle_3_deg 12.866 r_lrange_it 9.087 r_lrange_other 9.062 r_scangle_it 8.278 r_scangle_other 8.277 r_dihedral_angle_1_deg 7.074 r_scbond_other 6.817 r_scbond_it 6.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.245 r_dihedral_angle_4_deg 23.814 r_dihedral_angle_3_deg 12.866 r_lrange_it 9.087 r_lrange_other 9.062 r_scangle_it 8.278 r_scangle_other 8.277 r_dihedral_angle_1_deg 7.074 r_scbond_other 6.817 r_scbond_it 6.816 r_mcangle_it 3.782 r_mcangle_other 3.775 r_mcbond_it 3.165 r_mcbond_other 3.156 r_angle_refined_deg 1.517 r_angle_other_deg 1.473 r_symmetry_nbd_refined 0.409 r_nbd_other 0.303 r_symmetry_xyhbond_nbd_other 0.227 r_nbd_refined 0.214 r_symmetry_nbd_other 0.18 r_xyhbond_nbd_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.167 r_ncsr_local_group_1 0.101 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5919 Nucleic Acid Atoms Solvent Atoms 850 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement Aimless data reduction XSCALE data scaling PHASER phasing