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PseC aminotransferase involved in pseudoaminic acid biosynthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FN6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 293 protein (5 mg/ml) in buffer (20 mM citrate, pH 5.4, 0.1 M NaCl, 5% (v/v) glycerol, and 10 mM DTT) was incubated with 0.5 mM PLP. Crystals of the PseC-PLP complex were grown by mixing 1.5 microL protein and 1.5 microL reservoir solution (21% PEG 3350, 0.21 M sodium formate) by vapor diffusion against reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.79 55.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.4 α = 90 b = 153.3 β = 90 c = 70.7 γ = 90
Symmetry Space Group P 21 21 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 RIGAKU RAXIS HTC Osmic mirrors 2004-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 3 50 95.1 0.098 7.1 5 19466 19466 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.1
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 2FN6 3 50 19466 18470 996 98.46 0.19943 0.19632 0.2009 0.25794 0.2578 RANDOM 41.568
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] 0.87 -2.96 2.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.451 r_dihedral_angle_3_deg 14.776 r_dihedral_angle_4_deg 11.462 r_dihedral_angle_1_deg 5.249 r_scangle_it 2.632 r_mcangle_it 1.588 r_scbond_it 1.547 r_angle_refined_deg 1.062 r_mcbond_it 0.926 r_nbtor_refined 0.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.451 r_dihedral_angle_3_deg 14.776 r_dihedral_angle_4_deg 11.462 r_dihedral_angle_1_deg 5.249 r_scangle_it 2.632 r_mcangle_it 1.588 r_scbond_it 1.547 r_angle_refined_deg 1.062 r_mcbond_it 0.926 r_nbtor_refined 0.329 r_nbd_refined 0.235 r_symmetry_vdw_refined 0.223 r_symmetry_hbond_refined 0.209 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5921 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing