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Crystal Structure of Double Mutant Phenylalanine Ammonia-Lyase From Anabaena Variabilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NYN PDB entry 2NYN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 12-20% PEG1500 and 100 mM SPG (succinic acid, sodium dihydrogen phosphate, glycine), pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 42.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 195.153 α = 90 b = 78.054 β = 120.43 c = 156.758 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 200 CCD MARMOSAIC 325 mm CCD MIRRORS 2007-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.9183 SSRL BL11-1
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 2.2 134.8 97 0.07 122951 122951
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 2.2 2.25 92 0.39 2.1
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 PDB entry 2NYN 2.2 34.9 92108 90920 4763 92.56 0.21369 0.21039 0.2108 0.27638 0.276 RANDOM 31.548
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] 0.11 0.1 -0.05 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.242 r_dihedral_angle_4_deg 17.627 r_dihedral_angle_3_deg 15.795 r_dihedral_angle_1_deg 6.29 r_scangle_it 3.07 r_scbond_it 2.119 r_angle_refined_deg 1.501 r_mcangle_it 1.163 r_mcbond_it 0.753 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.242 r_dihedral_angle_4_deg 17.627 r_dihedral_angle_3_deg 15.795 r_dihedral_angle_1_deg 6.29 r_scangle_it 3.07 r_scbond_it 2.119 r_angle_refined_deg 1.501 r_mcangle_it 1.163 r_mcbond_it 0.753 r_nbtor_refined 0.303 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.211 r_symmetry_hbond_refined 0.209 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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 16468 Nucleic Acid Atoms Solvent Atoms 688 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing