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The closed conformation of ATP-dependent DNA ligase from Archaeoglobus fulgidus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CFM PDB ENTRY 2CFM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 294 100mM Tris-HCl, pH9.0, 0.4M sodium dihydrogen phosphate, 1.2M dipotassium hydrogen phosphate, 10mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.44 64.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.355 α = 90 b = 94.355 β = 90 c = 197.416 γ = 90
Symmetry Space Group P 41 21 2
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 210 2006-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A 1.0000 PAL/PLS 4A
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 2.3 20 100 0.089 36 40500
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) 2.3 2.38 100 0.44 5.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2CFM 2.3 20 36294 4007 99.84 0.221 0.215 0.277 0.2023 RANDOM 37.035
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] 1.62 1.62 -3.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.166 r_dihedral_angle_4_deg 19.356 r_dihedral_angle_3_deg 18.92 r_dihedral_angle_1_deg 7.246 r_scangle_it 2.765 r_scbond_it 1.622 r_angle_refined_deg 1.314 r_mcangle_it 1.189 r_mcbond_it 0.683 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.166 r_dihedral_angle_4_deg 19.356 r_dihedral_angle_3_deg 18.92 r_dihedral_angle_1_deg 7.246 r_scangle_it 2.765 r_scbond_it 1.622 r_angle_refined_deg 1.314 r_mcangle_it 1.189 r_mcbond_it 0.683 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.198 r_symmetry_hbond_refined 0.187 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.098 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4423 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms 20
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction PHASER phasing