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DNA targeting ADP-ribosyltransferase Pierisin-1, autoinhibitory form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CB4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 22% (v/v) t-butanol and 0.1M Tris-HCl pH8
Crystal Properties Matthews coefficient Solvent content 3.06 59.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.07 α = 90 b = 110.5 β = 91.2 c = 133.64 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD ADSC QUANTUM 315 2007-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 50 95 19.3 3.74 132451
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 2CB4 1.8 30.068 125934 6687 94.79 0.22487 0.224 0.2293 0.24141 0.2469 RANDOM 31.354
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] -0.69 -0.64 0.54 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.756 r_dihedral_angle_4_deg 13.126 r_dihedral_angle_3_deg 11.442 r_dihedral_angle_1_deg 5.93 r_long_range_B_refined 3.831 r_long_range_B_other 3.562 r_mcangle_it 1.657 r_mcangle_other 1.657 r_scangle_other 1.254 r_angle_refined_deg 1.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.756 r_dihedral_angle_4_deg 13.126 r_dihedral_angle_3_deg 11.442 r_dihedral_angle_1_deg 5.93 r_long_range_B_refined 3.831 r_long_range_B_other 3.562 r_mcangle_it 1.657 r_mcangle_other 1.657 r_scangle_other 1.254 r_angle_refined_deg 1.122 r_mcbond_it 0.903 r_mcbond_other 0.903 r_angle_other_deg 0.88 r_scbond_it 0.692 r_scbond_other 0.692 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7885 Nucleic Acid Atoms Solvent Atoms 588 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing