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HUman PARP14 (ARTD8)-Macro domain 1 in complex with adenosine-5-diphosphoribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SPV PDB ENTRY 1SPV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 293 30% PEGMME2000, 0.1M HEPES, 4mM ADP-RIBOSE, 4mM MAGNESIUM CHLORIDE, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.93 36.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.357 α = 90 b = 71.357 β = 90 c = 71.436 γ = 90
Symmetry Space Group P 43 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 RAYONIX MX-225 MIRRORS 2010-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.23 35 99.8 0.093 0.079 24.8 11.8 9427 30.5
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 2.23 2.29 99.6 0.623 0.325 5.5 12 667
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 (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 1SPV 2.23 31.92 8956 8956 472 100 0.212 0.208 0.2062 0.278 0.2676 RANDOM 21.92
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] 0.59 0.59 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.596 r_dihedral_angle_3_deg 16.094 r_dihedral_angle_4_deg 16.094 r_dihedral_angle_1_deg 6.486 r_scangle_it 4.248 r_scbond_it 2.516 r_angle_refined_deg 1.756 r_mcangle_it 1.676 r_angle_other_deg 0.913 r_mcbond_it 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.596 r_dihedral_angle_3_deg 16.094 r_dihedral_angle_4_deg 16.094 r_dihedral_angle_1_deg 6.486 r_scangle_it 4.248 r_scbond_it 2.516 r_angle_refined_deg 1.756 r_mcangle_it 1.676 r_angle_other_deg 0.913 r_mcbond_it 0.87 r_mcbond_other 0.181 r_chiral_restr 0.168 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1413 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 36
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling