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Redesign of a Phenylalanine Aminomutase into a beta-Phenylalanine Ammonia Lyase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YII PDB ENTRY 2YII
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 % TACSISMATE, 12 % W/V PEG 3350, 2 MM DTT
Crystal Properties Matthews coefficient Solvent content 2.29 46.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.295 α = 90 b = 145.837 β = 99.96 c = 99.413 γ = 90
Symmetry Space Group P 1 21 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 2011-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.5 48.9 98.1 0.12 6.2 2.3 94431 36.7
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 2.5 2.64 97.6 0.38 2.4 2.3
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 PDB ENTRY 2YII 2.5 48.9 89618 4716 97.99 0.21072 0.20885 0.2084 0.24637 0.2455 RANDOM 38.459
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] 2.56 2.44 -0.39 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.045 r_dihedral_angle_4_deg 15.511 r_dihedral_angle_3_deg 13.904 r_dihedral_angle_1_deg 4.46 r_angle_refined_deg 0.934 r_chiral_restr 0.06 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.045 r_dihedral_angle_4_deg 15.511 r_dihedral_angle_3_deg 13.904 r_dihedral_angle_1_deg 4.46 r_angle_refined_deg 0.934 r_chiral_restr 0.06 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 19724 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling