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Crystal structure of rubredoxin from piezophilic hyperthermophilic archaeon Pyrococcus yayanosii
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 VAPOR DIFFUSION AGAINST 3.2M NA,K PHOSPHATE, pH 7.0
Crystal Properties Matthews coefficient Solvent content 1.9 35.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.914 α = 90 b = 63.513 β = 90 c = 78.063 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 2023-11-15 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) Rpim I (All) 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 1.357 33.276 89.7 0.447 0.138 0.979 6.4 10.2 17219 20.31
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.357 1.5 57.5 3.708 1.216 0.837 1.5 9.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 1.36 33.28 17219 869 57.8 0.172 0.1718 0.213 0.2132 14.35
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] -0.033 0.343 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.169 r_dihedral_angle_1_deg 5.736 r_dihedral_angle_2_deg 5.215 r_scangle_it 4.985 r_scangle_other 4.983 r_scbond_it 3.265 r_scbond_other 3.264 r_mcangle_other 2.216 r_mcangle_it 2.205 r_angle_refined_deg 1.589
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.169 r_dihedral_angle_1_deg 5.736 r_dihedral_angle_2_deg 5.215 r_scangle_it 4.985 r_scangle_other 4.983 r_scbond_it 3.265 r_scbond_other 3.264 r_mcangle_other 2.216 r_mcangle_it 2.205 r_angle_refined_deg 1.589 r_mcbond_it 1.398 r_mcbond_other 1.372 r_angle_other_deg 0.565 r_nbd_refined 0.239 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.169 r_nbd_other 0.156 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbtor_other 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_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1233 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction Aimless data scaling HKL2Map phasing