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The 1.7 A crystal structure of Dronpa: a photoswitchable green fluorescent protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XSS PDB ENTRY 1XSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 23% PEG 3350, 0.1M Tris, 0.1M Magnesium Chloride, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.14 α = 90 b = 175.499 β = 90 c = 67.441 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID APS 17-ID
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 1.7 89.09 96.3 0.085 0.085 22.8 5.2 129416 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.704 1.748 95.6 0.573 0.573 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1XSS 1.7 89.09 2 2 129416 122748 6503 96.34 0.19922 0.19808 0.22093 RANDOM 19.289
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] -0.6 -0.51 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.706 r_dihedral_angle_4_deg 11.892 r_dihedral_angle_3_deg 11.589 r_dihedral_angle_1_deg 5.761 r_scangle_it 2.707 r_scbond_it 1.801 r_mcangle_it 1.138 r_angle_refined_deg 0.945 r_mcbond_it 0.662 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.706 r_dihedral_angle_4_deg 11.892 r_dihedral_angle_3_deg 11.589 r_dihedral_angle_1_deg 5.761 r_scangle_it 2.707 r_scbond_it 1.801 r_mcangle_it 1.138 r_angle_refined_deg 0.945 r_mcbond_it 0.662 r_nbtor_refined 0.298 r_nbd_refined 0.165 r_symmetry_vdw_refined 0.128 r_symmetry_hbond_refined 0.086 r_xyhbond_nbd_refined 0.078 r_chiral_restr 0.065 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_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 10295 Nucleic Acid Atoms Solvent Atoms 739 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing