☰ Navigation Tabs
Structure of a VgrG Vibrio cholerae toxin ACD domain in complex with ADP and Mg++
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DTF PDB ENTRY 4DTF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.3 293 300 nL of protein at 13mg/mL, 100 nL of 2.4 M AmSO4, 0.1 M Bi-Tris, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.61 65.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.46 α = 90 b = 128.46 β = 90 c = 76.39 γ = 90
Symmetry Space Group P 43 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 IMAGE PLATE MAR scanner 345 mm plate MIRRORS 2012-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR
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 2.25 50 100 0.053 21.4 4.2 28824 39.49
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 2.25 2.3 93.2 0.436 3.7 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 4DTF 2.25 40.62 28721 28721 1019 92.9 0.175 0.174 0.1761 0.196 0.199 RANDOM 37.25
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] -2.2882 -2.2882 4.5764
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.17 t_omega_torsion 3.23 t_angle_deg 1.08 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 19.17 t_omega_torsion 3.23 t_angle_deg 1.08 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 2757 Nucleic Acid Atoms Solvent Atoms 470 Heterogen Atoms 55
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing BUSTER refinement HKL-3000 data reduction XSCALE data scaling