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Human parp14 (artd8) - macro domain 2 in complex with adenosine-5-diphosphoribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IID PDB ENTRY 3IID
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.1 277 1.4M Ammonium Sulfate, 0.1M Sodium Acetate, 0.4M Sodium Chloride, 4mM ADP-ribose, 4mM Magnesium Chloride, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.89 57.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.35 α = 90 b = 66.35 β = 90 c = 110.69 γ = 120
Symmetry Space Group P 32 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 MAR CCD 165 mm mirrors 2010-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-5 0.9077 MAX II I911-5
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 2.2 30 99.9 0.149 0.122 14 9 14842 14842
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 2.2 2.3 99.9 0.584 0.391 4.2 9.1 1824
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 3IID 2.2 28.73 13357 13357 1484 100 0.19088 0.19088 0.18731 0.1925 0.22273 0.2261 RANDOM 14.088
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] 0.67 0.34 0.67 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.044 r_dihedral_angle_4_deg 20.401 r_dihedral_angle_3_deg 14.7 r_dihedral_angle_1_deg 5.358 r_scangle_it 3.19 r_scbond_it 1.824 r_angle_refined_deg 1.298 r_mcangle_it 1.155 r_angle_other_deg 0.83 r_mcbond_it 0.587
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.044 r_dihedral_angle_4_deg 20.401 r_dihedral_angle_3_deg 14.7 r_dihedral_angle_1_deg 5.358 r_scangle_it 3.19 r_scbond_it 1.824 r_angle_refined_deg 1.298 r_mcangle_it 1.155 r_angle_other_deg 0.83 r_mcbond_it 0.587 r_mcbond_other 0.109 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 1568 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 36
Software Software Software Name Purpose MxCuBE data collection BALBES phasing REFMAC refinement XDS data reduction XSCALE data scaling