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crystal structure of GFP-TYR151PYZ with an unnatural amino acid incorporation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GFL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.9 289 60~100mg/ml protein sample in 50 mM Hepes, pH 7.5, reservior solution:16~19% PEG 3000, 100mM Tris pH 8.9,0.2M calcium acetate, VAPOR DIFFUSION, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.04 39.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.717 α = 90 b = 50.809 β = 90 c = 62.364 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 90 CCD ADSC QUANTUM 315 2012-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U
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 1.23 50 98.7 0.09 0.077 23.5 9.5 63375 62551 3 3
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 (All) 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 1GFL 1.23 45.87 59944 59267 3167 98.87 0.17 0.16414 0.16293 0.1704 0.18773 0.1939 RANDOM 13.004
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] 1.82 -0.84 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.42 r_dihedral_angle_3_deg 11.22 r_dihedral_angle_1_deg 10.562 r_dihedral_angle_4_deg 8.929 r_sphericity_free 5.137 r_scangle_it 3.491 r_sphericity_bonded 2.795 r_scbond_it 2.339 r_mcangle_it 1.766 r_angle_refined_deg 1.474
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.42 r_dihedral_angle_3_deg 11.22 r_dihedral_angle_1_deg 10.562 r_dihedral_angle_4_deg 8.929 r_sphericity_free 5.137 r_scangle_it 3.491 r_sphericity_bonded 2.795 r_scbond_it 2.339 r_mcangle_it 1.766 r_angle_refined_deg 1.474 r_rigid_bond_restr 1.208 r_mcbond_it 1.123 r_chiral_restr 0.101 r_bond_refined_d 0.009 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_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1813 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-2000 data collection DENZO data reduction HKL-2000 data scaling CNS phasing