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Pyrococcus abyssi Rubredoxin @ 0.43 Angstrom resolution, Transferable Aspherical Atom Model (TAAM) refinement
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9TA4
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 = 24.73 α = 90 b = 39.237 β = 90 c = 45.14 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 19 Beryllium compound refractive lenses, proximal slits (20 cm from sample) 2025-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.38573 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 0.433 20.921 96.2 0.0562 0.0573 0.011 1 23.92 26.62 245905
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) 0.433 0.464 59.9 1.8678 1.923 0.4541 0.621 1.66 17.76 12295
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 0.434 20.92 245522 12376 85.1 0.0653 0.0651 0.0754 0.0693 0.079 RANDOM 4.65
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] -0.2461 -0.0451 0.2912
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.02 t_omega_torsion 6.74 t_angle_deg 2.59 t_bond_d 0.033 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 115 Heterogen Atoms 4
Software Software Software Name Purpose MxCuBE data collection XDS data reduction autoPROC data processing Aimless data scaling STARANISO data scaling BUSTER phasing BUSTER refinement