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Zinc Rubredoxin from Pyrococcus Furiosus at 140K, A2 Nterminus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9XZU Model from the same crystal
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 VAPOR DIFFUSION AGAINST 3.1 M NaCl with 3.6M Na,K PHOSPHATE, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.15 41.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.893 α = 90 b = 34.348 β = 90 c = 43.474 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 140 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 0.72929 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 0.83 26.95 93.6 0.048 0.02 1 17.4 6.5 37292 9.655
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 0.832 0.901 53.6 0.716 0.326 0.75 1.6 5.6
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 MOLECULAR REPLACEMENT THROUGHOUT 0.83 26.95 35416 1876 77.18 0.12749 0.12685 0.1188 0.13951 0.1282 RANDOM 7.941
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] 0.66 -4.91 4.25
RMS Deviations Key Refinement Restraint Deviation r_scangle_other 29.122 r_scbond_it 24.821 r_scbond_other 24.75 r_long_range_B_refined 24.132 r_long_range_B_other 17.158 r_mcangle_other 12.515 r_mcangle_it 12.222 r_dihedral_angle_3_deg 12.098 r_mcbond_it 11.518 r_rigid_bond_restr 7.644
RMS Deviations Key Refinement Restraint Deviation r_scangle_other 29.122 r_scbond_it 24.821 r_scbond_other 24.75 r_long_range_B_refined 24.132 r_long_range_B_other 17.158 r_mcangle_other 12.515 r_mcangle_it 12.222 r_dihedral_angle_3_deg 12.098 r_mcbond_it 11.518 r_rigid_bond_restr 7.644 r_dihedral_angle_1_deg 5.948 r_mcbond_other 3.604 r_angle_refined_deg 1.835 r_angle_other_deg 0.612 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_2_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 413 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction Aimless data scaling PHASER phasing