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Crystal structure of C. violaceum phenylalanine hydroxylase D139K mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LTU pdb entry 1LTU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 100 mM Na-HEPES pH 7.0, 10 mM Magnesium chloride hexahydrate, 5 mM Nickel(II) chloride hexahydrate, 15% w/v polyethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.87 34.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.813 α = 76.59 b = 38.587 β = 72.84 c = 47.665 γ = 85.46
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 MAR scanner 300 mm plate 2012-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.35 50 95.4 0.068 0.068 15.9 4 50858 48519 2 2
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 1.35 1.37 92.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1LTU 1.35 21.81 50734 48263 2595 95.13 0.16157 0.15967 0.19836 0.2165 RANDOM 17.757
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] 0.53 -0.84 1.31 0.34 -0.65 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.534 r_sphericity_free 22.08 r_sphericity_bonded 14.71 r_dihedral_angle_4_deg 13.722 r_dihedral_angle_3_deg 12.828 r_dihedral_angle_1_deg 5.756 r_rigid_bond_restr 4.989 r_angle_refined_deg 1.403 r_chiral_restr 0.09 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.534 r_sphericity_free 22.08 r_sphericity_bonded 14.71 r_dihedral_angle_4_deg 13.722 r_dihedral_angle_3_deg 12.828 r_dihedral_angle_1_deg 5.756 r_rigid_bond_restr 4.989 r_angle_refined_deg 1.403 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2157 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 1
Software Software Software Name Purpose HKL-3000 data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling