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Structure of the transaminase PhnW from Vibrio vulnificus in complex with PLP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Crystals of VvPhnW were grown in drops containing 1.5 ul of protein solution (25 mg/ml in the buffer 10 mM HEPES pH 7.5, 3.4mM PLP ,150 mM NaCl, 1 mM DTT) and 1.5 ul of reservoir solution (100 mM Bis-Tris pH6.5, 25% (w/v) PEG3350).
Crystal Properties Matthews coefficient Solvent content 2.85 56.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.69 α = 90 b = 92.69 β = 90 c = 93.052 γ = 120
Symmetry Space Group P 32 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 PILATUS 6M 2024-05-13 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 2.401 60.78 100 0.084 0.087 0.021 0.999 18.5 18.2 18507
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 2.401 2.442 100 1.178 1.209 0.268 0.876 2.1 20.1
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 2.401 60.78 18505 929 100 0.187 0.186 0.1886 0.214 0.2095 RANDOM 82
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] 1.7078 1.7078 -3.4157
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.39 t_omega_torsion 3.25 t_angle_deg 1.13 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 19.39 t_omega_torsion 3.25 t_angle_deg 1.13 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 2797 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 15
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing