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Crystal structure of ADP-ribosyltransferase Vis in complex with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Y1W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 30% Jeffamine ED-2001, 0.1 M Hepes
Crystal Properties Matthews coefficient Solvent content 2.61 52.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.7 α = 90 b = 52 β = 90 c = 100.4 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2011-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 20 94.7 0.0445 25.84 6.25 23562
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 1.8 1.9 91.8 0.1799 8.67 5.24
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4Y1W 1.8 18.63 23524 1191 94.81 0.1767 0.1751 0.2054 0.2242 RANDOM 23.386
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] -0.47 1 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.06 r_dihedral_angle_4_deg 14.998 r_dihedral_angle_3_deg 12.927 r_dihedral_angle_1_deg 5.832 r_angle_refined_deg 1.424 r_angle_other_deg 0.768 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.06 r_dihedral_angle_4_deg 14.998 r_dihedral_angle_3_deg 12.927 r_dihedral_angle_1_deg 5.832 r_angle_refined_deg 1.424 r_angle_other_deg 0.768 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1756 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 44
Software Software Software Name Purpose XDS data reduction PDB_EXTRACT data extraction REFMAC refinement SHELX phasing PHASER phasing XPREP data reduction