☰ Navigation Tabs
Calcium bound to the Holliday junction sequence d(TCGGCGCCGA)4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L4J PDB entry 1L4J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 CaCl2, MPD, NaCacodylate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K, temperature 290.0K
Crystal Properties Matthews coefficient Solvent content 2.27 45.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.97 α = 90 b = 24.17 β = 110.37 c = 73.89 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 100 CCD OXFORD SAPPHIRE CCD multilayer optics M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.5418
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 2.1 16.347 99.41 0.062 11.44 3.9 6643 6622 1 1 17.122
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) 2.1 2.155 99.41 0.194 2.35 3 1773
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1L4J 2.1 16.347 6622 6622 311 99.41 0.218 0.218 0.214 0.2118 0.306 0.3022 RANDOM 17.122
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] -1.24 0.06 1.3 -0.02
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.285 r_scangle_it 1.079 r_scbond_it 0.716 r_nbtor_refined 0.293 POTENTIAL METAL-ION REFINED ATOMS (A) 0.163 r_nbd_refined 0.162 r_xyhbond_nbd_refined 0.119 r_symmetry_vdw_refined 0.098 r_symmetry_hbond_refined 0.071 r_chiral_restr 0.053
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.285 r_scangle_it 1.079 r_scbond_it 0.716 r_nbtor_refined 0.293 POTENTIAL METAL-ION REFINED ATOMS (A) 0.163 r_nbd_refined 0.162 r_xyhbond_nbd_refined 0.119 r_symmetry_vdw_refined 0.098 r_symmetry_hbond_refined 0.071 r_chiral_restr 0.053 r_bond_refined_d 0.005 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 808 Solvent Atoms 183 Heterogen Atoms 4
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction CrysalisPro data collection CrysalisPro data reduction MOLREP phasing REFMAC refinement