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Crystal structure of native PARN nuclease domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A1R PDB ENTRY 2A1R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 PEG3350, 0.2M ammonium tartrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.42 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 205.54 α = 90 b = 123.016 β = 112.59 c = 82.844 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 ADSC QUANTUM 210 2004-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9791 ESRF ID29
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 2.6 50 99.5 0.079 6.2 3.5 58187 58173 2 2 69.76
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 2.6 2.69 99.6 0.628 2 3.5 5683
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 2A1R 2.6 20 3 3 58173 56251 1780 99.41 0.243 0.21971 0.21864 0.2248 0.25362 0.2567 RANDOM 52.465
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 2.19 2.09 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.132 r_scangle_it 2.613 r_mcangle_it 1.51 r_scbond_it 1.48 r_angle_refined_deg 1.334 r_angle_other_deg 0.815 r_mcbond_it 0.796 r_symmetry_vdw_other 0.247 r_nbd_other 0.228 r_symmetry_hbond_refined 0.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.132 r_scangle_it 2.613 r_mcangle_it 1.51 r_scbond_it 1.48 r_angle_refined_deg 1.334 r_angle_other_deg 0.815 r_mcbond_it 0.796 r_symmetry_vdw_other 0.247 r_nbd_other 0.228 r_symmetry_hbond_refined 0.225 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.195 r_xyhbond_nbd_refined 0.188 r_nbtor_other 0.088 r_chiral_restr 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12876 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing