☰ Navigation Tabs
Crystal structure of H-NOX protein from Nostoc sp V52W/L67W double-mutant.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DX6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 289 sodium phosphate, potassium phosphate
Crystal Properties Matthews coefficient Solvent content 3 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.172 α = 90 b = 65.172 β = 90 c = 103.264 γ = 120
Symmetry Space Group P 32 2 1
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 Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 2018-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
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 2.6 30 98 0.139 9.1 4.8 8033 47.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.72 99 0.91 2.1 4.9
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 6DX6 2.6 30 7622 385 97.43 0.20972 0.2068 0.2114 0.25943 0.2474 RANDOM 46.451
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] 1.28 0.64 1.28 -4.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.708 r_dihedral_angle_3_deg 21.592 r_dihedral_angle_4_deg 18.785 r_long_range_B_refined 9.924 r_long_range_B_other 9.923 r_scangle_other 8.09 r_dihedral_angle_1_deg 6.507 r_mcangle_it 5.606 r_mcangle_other 5.604 r_scbond_other 5.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.708 r_dihedral_angle_3_deg 21.592 r_dihedral_angle_4_deg 18.785 r_long_range_B_refined 9.924 r_long_range_B_other 9.923 r_scangle_other 8.09 r_dihedral_angle_1_deg 6.507 r_mcangle_it 5.606 r_mcangle_other 5.604 r_scbond_other 5.253 r_scbond_it 5.249 r_mcbond_it 3.656 r_mcbond_other 3.656 r_angle_refined_deg 1.865 r_angle_other_deg 0.864 r_chiral_restr 0.121 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 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 1503 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling FFT phasing