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Crystal Structure of Human DNA Ligase I bound to 5'-adenylated, nicked DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.8 298 PEG 4000, sodium acetate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.94 69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.889 α = 90 b = 161.889 β = 90 c = 88.455 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2003-10-25 M MAD 2 1 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 NSLS X25 2 SYNCHROTRON NSLS BEAMLINE X25 0.9787, 0.9791, 0.9635, 1.1 NSLS X25 3 SYNCHROTRON NSLS BEAMLINE X12C 1.006, 1.011, 0.969, 1.1 NSLS X12C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3 50 99.1 0.078 23.1 10 26365 26365 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 99.9 0.48 5
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 MAD THROUGHOUT 3 20 24943 1301 50 0.23626 0.23459 0.215 0.26833 0.2198 RANDOM 41.591
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] -3.65 -1.82 -3.65 5.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.603 r_scangle_it 2.597 r_scbond_it 1.587 r_angle_refined_deg 1.524 r_mcangle_it 0.938 r_mcbond_it 0.458 r_symmetry_vdw_refined 0.316 r_nbd_refined 0.254 r_chiral_restr 0.083 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.603 r_scangle_it 2.597 r_scbond_it 1.587 r_angle_refined_deg 1.524 r_mcangle_it 0.938 r_mcbond_it 0.458 r_symmetry_vdw_refined 0.316 r_nbd_refined 0.254 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4894 Nucleic Acid Atoms 813 Solvent Atoms Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement ACE data reduction HKL-2000 data scaling SHARP phasing