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Re-refinement of PDB entry 5RNT - ribonuclease T1 with guanosine-3',5'-diphosphate and phosphate ion bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SYU
Crystallization Crystal Properties Matthews coefficient Solvent content 2.43 49.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.47 α = 90 b = 86.47 β = 90 c = 86.47 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3SYU 3.19 43.24 1874 102 98.89 0.2035 0.2018 0.1718 0.2372 0.2057 RANDOM 26.6536
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]
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.3 t_omega_torsion 3.47 t_angle_deg 1 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.3 t_omega_torsion 3.47 t_angle_deg 1 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 776 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 34
Software Software Software Name Purpose BUSTER-TNT refinement PDB_EXTRACT data extraction MOLREP phasing BUSTER refinement