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Crystal structure of phenylalanine hydroxylase from Chromobacterium violaceum bound to cobalt
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 0.1M Na-HEPES, 0.001M Magnesium chloride hexahydrate, 15% w/v PEG 3,350, 0.1M Hexammine cobalt (III) chloride, 1.0M Guanidine hydrochloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.86 33.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.885 α = 76.49 b = 38.577 β = 73.15 c = 47.877 γ = 85.39
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 2011-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
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 1.5 50 95.1 0.031 0.031 24.2 1.9 37372 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 1.5 1.53 82.5
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 1LTU 1.5 37.51 37348 35492 1875 95.03 0.17275 0.17087 0.2033 0.20965 0.2433 RANDOM 15.696
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.642 r_dihedral_angle_3_deg 14.077 r_dihedral_angle_4_deg 13.631 r_dihedral_angle_1_deg 5.384 r_scangle_it 3.77 r_sphericity_free 3.653 r_sphericity_bonded 2.596 r_scbond_it 2.501 r_mcangle_it 1.72 r_rigid_bond_restr 1.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.642 r_dihedral_angle_3_deg 14.077 r_dihedral_angle_4_deg 13.631 r_dihedral_angle_1_deg 5.384 r_scangle_it 3.77 r_sphericity_free 3.653 r_sphericity_bonded 2.596 r_scbond_it 2.501 r_mcangle_it 1.72 r_rigid_bond_restr 1.404 r_angle_refined_deg 1.324 r_mcbond_it 1.012 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2220 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 2
Software Software Software Name Purpose HKL-3000 data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling