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Rubredoxin from Pyrococcus Furiosus at 200K, Alanine-2 N terminus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9XZU
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 2.16 41.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.961 α = 90 b = 34.378 β = 90 c = 43.555 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 200 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 0.86 26.985 94.1 0.048 0.02 0.999 16.8 6.6 34125 10.559
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 0.867 0.882 0.793 0.332 0.755 1.6
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 0.86 26.98 32434 1690 77.93 0.13597 0.13529 0.1412 0.14947 0.1525 RANDOM 8.465
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] 0.48 -1.52 1.04
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 27.992 r_long_range_B_other 16.321 r_dihedral_angle_3_deg 9.909 r_rigid_bond_restr 7.777 r_scangle_other 7.477 r_dihedral_angle_1_deg 5.833 r_scbond_it 5.715 r_scbond_other 5.631 r_mcangle_other 3.462 r_mcangle_it 3.394
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 27.992 r_long_range_B_other 16.321 r_dihedral_angle_3_deg 9.909 r_rigid_bond_restr 7.777 r_scangle_other 7.477 r_dihedral_angle_1_deg 5.833 r_scbond_it 5.715 r_scbond_other 5.631 r_mcangle_other 3.462 r_mcangle_it 3.394 r_mcbond_it 2.58 r_mcbond_other 2.387 r_angle_refined_deg 1.926 r_angle_other_deg 0.669 r_chiral_restr 0.098 r_bond_refined_d 0.012 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 135 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction Aimless data scaling PHASER phasing