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Rubredoxin from Pyrococcus Furiosus at 383K, formyl-Methionine N-terminus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9Y2E 100K fMET N-terminus
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 2.2 42.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.266 α = 90 b = 34.813 β = 90 c = 43.214 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 383 PIXEL DECTRIS EIGER X 16M 2025-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
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 1.529 27.11 90.4 0.337 0.104 0.965 7.7 12.4 6867 30.773
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 1.529 1.638 38.8 4.954 1.345 0.17 1.5 14.6
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 1.53 27.11 6526 341 83.47 0.1467 0.14467 0.1576 0.19009 0.195 RANDOM 28.975
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] 1.56 -1.12 -0.44
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 19.622 r_long_range_B_refined 19.607 r_scangle_other 17.328 r_dihedral_angle_3_deg 15.936 r_scbond_it 12.965 r_scbond_other 12.867 r_mcangle_other 10.016 r_mcangle_it 10.002 r_mcbond_it 7.473 r_mcbond_other 7.452
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 19.622 r_long_range_B_refined 19.607 r_scangle_other 17.328 r_dihedral_angle_3_deg 15.936 r_scbond_it 12.965 r_scbond_other 12.867 r_mcangle_other 10.016 r_mcangle_it 10.002 r_mcbond_it 7.473 r_mcbond_other 7.452 r_dihedral_angle_1_deg 5.678 r_rigid_bond_restr 4.058 r_dihedral_angle_2_deg 1.907 r_angle_refined_deg 1.692 r_angle_other_deg 0.609 r_chiral_restr 0.078 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_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 423 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction Aimless data scaling PHASER phasing