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Pyrococcus abyssi Rubredoxin @ 0.55 Angstrom resolution, 50 kGy structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YK4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 291 3.6 - 3.8 M Sodium Malonate (pH 6.0)
Crystal Properties Matthews coefficient Solvent content 1.8 29.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.793 α = 90 b = 39.074 β = 90 c = 44.895 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 100 PIXEL DECTRIS EIGER2 X CdTe 16M 22 Beryllium compound refractive lenses, proximal slits (20 cm from sample) 2025-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.4640 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 0.545 29.474 94.2 0.0479 0.0498 0.0135 1 23.57 13.54 117913
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.545 0.586 59.5 1.4562 1.5124 0.4058 0.705 1.71 13.69
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 FOURIER SYNTHESIS THROUGHOUT 0.545 29.47 117913 5883 80.9 0.0767 0.0763 0.0763 0.0851 0.0836 RANDOM 5.76
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] -0.4313 0.107 0.3243
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.17 t_omega_torsion 6.52 t_angle_deg 2.21 t_bond_d 0.028 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 433 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 1
Software Software Software Name Purpose MxCuBE data collection XDS data reduction autoPROC data processing Aimless data scaling STARANISO data scaling BUSTER phasing BUSTER refinement