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Crystal structure of rubredoxin from psychrophilic bacterium Polaromonas glacialis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 VAPOR DIFFUSION AGAINST 1.5 M AMMONIUM SULFATE, pH 8.5
Crystal Properties Matthews coefficient Solvent content 3.25 62.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.897 α = 90 b = 73.897 β = 90 c = 199.351 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 EIGER X 16M 2023-12-15 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 1.83 69.29 95.3 0.277 0.054 0.998 14.1 54.1 36053 20.709
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 1.83 2.042 69.9 6.053 0.862 0.608 1.6 47.9
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-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.83 69.29 34216 1837 72.97 0.17226 0.17069 0.1816 0.201 0.2087 RANDOM 44.029
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] -0.06 -0.06 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.496 r_dihedral_angle_3_deg 12.744 r_long_range_B_refined 9.482 r_long_range_B_other 9.48 r_scangle_other 8.861 r_scbond_it 7.487 r_scbond_other 7.485 r_dihedral_angle_1_deg 6.262 r_mcangle_other 4.958 r_mcangle_it 4.941
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.496 r_dihedral_angle_3_deg 12.744 r_long_range_B_refined 9.482 r_long_range_B_other 9.48 r_scangle_other 8.861 r_scbond_it 7.487 r_scbond_other 7.485 r_dihedral_angle_1_deg 6.262 r_mcangle_other 4.958 r_mcangle_it 4.941 r_mcbond_it 4.015 r_mcbond_other 4.013 r_angle_refined_deg 1.704 r_angle_other_deg 0.557 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2920 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction Aimless data scaling HKL2Map phasing