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Rubredoxin from Pyrococcus Furiosus at 180K, Alanine-2 N terminus
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 2.16 41.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.923 α = 90 b = 34.357 β = 90 c = 43.519 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 180 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 0.852 26.966 94 0.047 0.02 1 17.2 6.6 35436 10.048
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 0.852 0.916 0.745 0.32 0.782 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 0.852 26.966 33755 1681 78.32 0.13135 0.13038 0.1374 0.15036 0.1571 RANDOM 7.356
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] 0.27 -1.07 0.81
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.653 r_long_range_B_other 10.045 r_dihedral_angle_3_deg 9.498 r_scangle_other 6.741 r_rigid_bond_restr 6.064 r_dihedral_angle_1_deg 5.95 r_scbond_it 5.025 r_scbond_other 4.688 r_mcangle_other 3.358 r_mcangle_it 3.275
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.653 r_long_range_B_other 10.045 r_dihedral_angle_3_deg 9.498 r_scangle_other 6.741 r_rigid_bond_restr 6.064 r_dihedral_angle_1_deg 5.95 r_scbond_it 5.025 r_scbond_other 4.688 r_mcangle_other 3.358 r_mcangle_it 3.275 r_mcbond_it 2.518 r_mcbond_other 2.314 r_angle_refined_deg 1.895 r_angle_other_deg 0.632 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 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 141 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction Aimless data scaling PHASER phasing