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Oceanobacillus iheyensis macrodomain mutant G37V with ADPR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SPV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.2 M ammonium sulfate, 0.1 M MES pH 6.5 and 30% (w/v) PEGMME 5K
Crystal Properties Matthews coefficient Solvent content 2.7 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.646 α = 90 b = 109.646 β = 90 c = 109.646 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M KB mirror 2014-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9795 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) 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 1.35 40 100 0.07 0.95 22.2 12.2 47986 14.15
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 1.35 1.39 100 0.404 6.2 12
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1spv 1.35 40 45534 2427 99.99 0.15566 0.15424 0.1633 0.18206 0.1884 RANDOM 18.227
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.089 r_sphericity_free 25.803 r_dihedral_angle_3_deg 10.972 r_sphericity_bonded 10.449 r_dihedral_angle_4_deg 7.282 r_dihedral_angle_1_deg 6.392 r_long_range_B_refined 3.075 r_long_range_B_other 3.074 r_scangle_other 2.449 r_scbond_it 2.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.089 r_sphericity_free 25.803 r_dihedral_angle_3_deg 10.972 r_sphericity_bonded 10.449 r_dihedral_angle_4_deg 7.282 r_dihedral_angle_1_deg 6.392 r_long_range_B_refined 3.075 r_long_range_B_other 3.074 r_scangle_other 2.449 r_scbond_it 2.018 r_scbond_other 2.017 r_mcangle_it 1.93 r_mcangle_other 1.929 r_angle_refined_deg 1.687 r_mcbond_it 1.459 r_mcbond_other 1.457 r_rigid_bond_restr 1.234 r_angle_other_deg 1.053 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.003 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1403 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing