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Crystal structure of PARN nuclease domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 PEG 3350, 0.2M ammonium tartrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.68 53.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.778 α = 90 b = 92.401 β = 90 c = 159.642 γ = 90
Symmetry Space Group P 21 21 21
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 MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9791, 0.9793, 0.9762 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 95.7 0.078 7.6 5 36514 36318 2 2 56.2
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 2.64 2.71 97.3 0.456 3.2 4.5 2353
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MAD THROUGHOUT 2.6 20 2 36514 31218 1610 97.24 0.2208 0.21909 0.21823 0.2229 0.23561 0.2352 RANDOM 49.222
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] 3.98 -5.57 1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.546 r_scangle_it 3.144 r_mcangle_it 1.997 r_scbond_it 1.772 r_angle_refined_deg 1.292 r_mcbond_it 1.054 r_angle_other_deg 0.794 r_symmetry_vdw_other 0.257 r_nbd_other 0.232 r_nbd_refined 0.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.546 r_scangle_it 3.144 r_mcangle_it 1.997 r_scbond_it 1.772 r_angle_refined_deg 1.292 r_mcbond_it 1.054 r_angle_other_deg 0.794 r_symmetry_vdw_other 0.257 r_nbd_other 0.232 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.201 r_xyhbond_nbd_refined 0.17 r_symmetry_hbond_refined 0.121 r_nbtor_other 0.087 r_chiral_restr 0.076 r_bond_refined_d 0.012 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 4799 Nucleic Acid Atoms 126 Solvent Atoms 153 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling SnB phasing