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PBP AccA from A. vitis S4 in complex with Agrocinopine C-like
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZEB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 292 PEG 8000, Tris-HCl
Crystal Properties Matthews coefficient Solvent content 1.9 35.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.83 α = 90 b = 60.71 β = 90 c = 151.39 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 PIXEL DECTRIS EIGER X 9M 2019-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980101 SOLEIL PROXIMA 2
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 1.398 47.36 98.9 0.082 0.99 14.19 11 85091
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 1.398 1.48 2.364 0.459
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.398 20.37 85091 4255 98.6 0.1911 0.1897 0.1833 0.2182 0.2128 RANDOM 33.11
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] -3.9512 4.1946 -0.2434
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.23 t_omega_torsion 5 t_angle_deg 1.13 t_bond_d 0.011 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3814 Nucleic Acid Atoms Solvent Atoms 403 Heterogen Atoms 38
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing