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Rubredoxin from Pyrococcus Furiosus at 313K, 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 2.25 43.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.356 α = 90 b = 34.915 β = 90 c = 43.919 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 313 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 1.41 27.331 90.7 0.111 0.033 0.997 11 12.5 8608 29.169
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 1.413 1.52 42.4 1.635 0.46 0.685 1.3 13.3
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 1.41 27.33 8173 434 81.27 0.15316 0.15104 0.1504 0.19537 0.1943 RANDOM 24.718
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] 0.14 0.3 -0.45
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 21.021 r_long_range_B_other 20.257 r_scangle_other 15.594 r_scbond_it 11.373 r_scbond_other 11.176 r_dihedral_angle_3_deg 10.859 r_mcangle_other 10.575 r_mcangle_it 10.534 r_mcbond_it 7.698 r_mcbond_other 7.658
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 21.021 r_long_range_B_other 20.257 r_scangle_other 15.594 r_scbond_it 11.373 r_scbond_other 11.176 r_dihedral_angle_3_deg 10.859 r_mcangle_other 10.575 r_mcangle_it 10.534 r_mcbond_it 7.698 r_mcbond_other 7.658 r_dihedral_angle_1_deg 6.346 r_rigid_bond_restr 4.828 r_dihedral_angle_2_deg 3.214 r_angle_refined_deg 1.702 r_angle_other_deg 0.591 r_chiral_restr 0.079 r_bond_refined_d 0.009 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 46 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction Aimless data scaling PHASER phasing