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Crystal Structure of the Lambda Xis-DNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RH6 PDB ENTRY 1RH6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 30% Polyethylene Glycol monomethyl ether 2000, 0.2 M Ammonium Sulfate and 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.14 42.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.483 α = 90 b = 57.483 β = 90 c = 163.613 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 IMAGE PLATE RIGAKU RAXIS IV Mirrors 2004-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.9 80 97.8 0.071 20.6 10.32 15654 15654 37.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 82.5 0.409 0.409 3.71 5.7 1330
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 1RH6 1.9 54.23 15573 779 97.94 0.194 0.191 0.1863 0.248 0.2344 RANDOM 26.393
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] 1.33 0.66 1.33 -1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.682 r_dihedral_angle_4_deg 19.833 r_dihedral_angle_3_deg 17.288 r_dihedral_angle_1_deg 5.634 r_scangle_it 3.113 r_scbond_it 2.342 r_angle_refined_deg 2.17 r_mcangle_it 1.433 r_angle_other_deg 1.229 r_mcbond_it 1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.682 r_dihedral_angle_4_deg 19.833 r_dihedral_angle_3_deg 17.288 r_dihedral_angle_1_deg 5.634 r_scangle_it 3.113 r_scbond_it 2.342 r_angle_refined_deg 2.17 r_mcangle_it 1.433 r_angle_other_deg 1.229 r_mcbond_it 1.2 r_mcbond_other 0.287 r_symmetry_vdw_other 0.263 r_nbd_other 0.219 r_nbtor_refined 0.212 r_symmetry_hbond_refined 0.209 r_symmetry_vdw_refined 0.206 r_nbd_refined 0.183 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.098 r_nbtor_other 0.086 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 898 Nucleic Acid Atoms 732 Solvent Atoms 174 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection EPMR phasing