☰ Navigation Tabs
Structure of the PBP AgaA in complex with agropinic acid from A.tumefacien R10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F1Q 3F1Q and 1DPP experimental model PDB 1DPP 3F1Q and 1DPP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 1.8 M AS, 0.1 M Mes pH 6.5, 0.2 M Zn acetate
Crystal Properties Matthews coefficient Solvent content 3.02 59.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.26 α = 90 b = 89.26 β = 90 c = 285.85 γ = 120
Symmetry Space Group P 65 2 2
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 2M 2016-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.65 52.48 99.9 0.132 19.2 20 82437 26.82
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.74 2.052
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 3F1Q and 1DPP 1.65 52.48 82180 4109 99.4 0.157 0.156 0.174 0.1635 RANDOM 29.65
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] 1.4528 1.4528 -2.9056
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.63 t_omega_torsion 3.89 t_angle_deg 0.97 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.63 t_omega_torsion 3.89 t_angle_deg 0.97 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3837 Nucleic Acid Atoms Solvent Atoms 470 Heterogen Atoms 167
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing