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Oryza sativa APL macrodomain in complex with ADP-ribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LW6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 293 25% PEG 1500 + 0.1 M SPG buffer (succinic acid, sodium phosphate monobasic monohydrate and glycine)
Crystal Properties Matthews coefficient Solvent content 2.32 46.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.496 α = 90 b = 91.318 β = 103.32 c = 62.882 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 PIXEL DECTRIS PILATUS 6M-F 2015-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.65 56.31 97.4 0.08 0.996 12.8 6.7 47191
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 77.7 0.406 0.875 3.2 5.2
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 5LW6 1.65 56.31 44846 2344 97.16 0.1564 0.15477 0.1679 0.18727 0.1978 RANDOM 24.533
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] -1.37 0.31 0.14 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.801 r_dihedral_angle_4_deg 19.214 r_dihedral_angle_3_deg 14.553 r_long_range_B_refined 7.94 r_long_range_B_other 7.871 r_dihedral_angle_1_deg 5.965 r_scangle_other 5.939 r_scbond_it 3.957 r_scbond_other 3.957 r_mcangle_other 3.357
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.801 r_dihedral_angle_4_deg 19.214 r_dihedral_angle_3_deg 14.553 r_long_range_B_refined 7.94 r_long_range_B_other 7.871 r_dihedral_angle_1_deg 5.965 r_scangle_other 5.939 r_scbond_it 3.957 r_scbond_other 3.957 r_mcangle_other 3.357 r_mcangle_it 3.355 r_mcbond_it 2.319 r_mcbond_other 2.277 r_angle_refined_deg 1.564 r_angle_other_deg 0.958 r_chiral_restr 0.101 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3113 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing