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Crystal structure of VvPlpA G389N from Vibrio vulnificus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JKZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 4 mg/ml in 10 mM HEPES, 150 mM NaCl, pH 7.5 was mixed with the reservoir solution (200 mM potassium sodium tartrate tetrahydrate, 180 mM NDSB-201, 14% polyethylene glycol 1500, and 5% glycerol)
Crystal Properties Matthews coefficient Solvent content 2.9 57.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.946 α = 90 b = 64.551 β = 116.55 c = 160.649 γ = 90
Symmetry Space Group C 1 2 1
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 PILATUS3 6M 2018-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9791 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.298 83.68 91.9 0.054 0.059 0.023 0.998 21.8 6.6 63445 42.41
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.298 2.337 76.2 0.208 0.229 0.095 0.998 5.9
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 6JKZ 2.3 46 63327 3159 92 0.175 0.174 0.1723 0.207 0.2045 RANDOM 42.96
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] -2.5195 -8.4921 10.2175 -7.698
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.55 t_omega_torsion 3.05 t_angle_deg 0.99 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 18.55 t_omega_torsion 3.05 t_angle_deg 0.99 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 9505 Nucleic Acid Atoms Solvent Atoms 468 Heterogen Atoms 148
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing