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Structure of Bacterial DNA Ligase with small-molecule ligand pyrimidin-2-amine (AT371) in an alternate binding site.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CC5 PDB ENTRY 4CC5
Crystallization Crystal Properties Matthews coefficient Solvent content 2.36 47.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.871 α = 90 b = 39.29 β = 90.46 c = 48.645 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 PIXEL DECTRIS PILATUS 2010-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2 85.9 98.6 0.08 11.2 3.4 22674 -3.7 23.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 99.8 0.15 7
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 PDB ENTRY 4CC5 2 85.93 21955 1151 98.3 0.1561 0.1531 0.1562 0.209 0.2207 RANDOM 28.17
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] 5.4428 1.0741 -6.6831 1.2403
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.15 t_omega_torsion 5.79 t_angle_deg 0.97 t_bond_d 0.011 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.15 t_omega_torsion 5.79 t_angle_deg 0.97 t_bond_d 0.011 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 2432 Nucleic Acid Atoms Solvent Atoms 510 Heterogen Atoms 17
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling PHASER phasing