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An activated, tetrameric gamma-delta resolvase: Hin chimaera bound to cleaved DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZR4 PDB ENTRY 1ZR4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 PROTEIN: DNA stock in 300 mM NaCl, 15 mM Tris-HCl, 0.05-0.15 M Mg Formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.19 70.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.138 α = 90 b = 137.687 β = 90 c = 83.473 γ = 90
Symmetry Space Group P 21 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 315 2003-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12B 1.05 NSLS X12B
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 3.5 50 96.5 0.091 16189 16189 -3
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 3.5 3.63 84.3 0.759 1.2 1380
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 1ZR4 3.5 20 15177 15177 802 96.97 0.28213 0.28213 0.28003 0.2769 0.32265 0.3229 RANDOM 173.333
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] -5.23 -11.97 17.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.146 r_dihedral_angle_3_deg 21.044 r_dihedral_angle_4_deg 13.706 r_dihedral_angle_1_deg 5.582 r_scangle_it 4.246 r_mcangle_it 3.76 r_scbond_it 2.758 r_mcbond_it 2.002 r_angle_refined_deg 1.157 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.146 r_dihedral_angle_3_deg 21.044 r_dihedral_angle_4_deg 13.706 r_dihedral_angle_1_deg 5.582 r_scangle_it 4.246 r_mcangle_it 3.76 r_scbond_it 2.758 r_mcbond_it 2.002 r_angle_refined_deg 1.157 r_nbtor_refined 0.298 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2788 Nucleic Acid Atoms 1344 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection SCALEPACK data scaling CNS phasing