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Biochemical properties and crystal structure of a novel beta- phenylalanine aminotransferase from Variovorax paradoxus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other CBF3 HOLO ENZYME STRUCTURE
Crystallization Crystal Properties Matthews coefficient Solvent content 2.39 48.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.67 α = 90 b = 99.88 β = 90 c = 104.79 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2010-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.28 66.31 99.8 0.1 10.9 4 43283 22.4
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 2.28 2.4 99.8 0.16 7.5 4
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 CBF3 HOLO ENZYME STRUCTURE 2.28 72.3 41060 2170 99.73 0.18422 0.18211 0.1821 0.22476 0.2258 RANDOM 20.104
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] 0.09 -0.2 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.47 r_dihedral_angle_4_deg 20.17 r_dihedral_angle_3_deg 15.514 r_dihedral_angle_1_deg 5.45 r_scangle_it 2.175 r_scbond_it 1.235 r_angle_refined_deg 1.105 r_mcangle_it 0.67 r_mcbond_it 0.327 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.47 r_dihedral_angle_4_deg 20.17 r_dihedral_angle_3_deg 15.514 r_dihedral_angle_1_deg 5.45 r_scangle_it 2.175 r_scbond_it 1.235 r_angle_refined_deg 1.105 r_mcangle_it 0.67 r_mcbond_it 0.327 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6495 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing