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Crystal structure of yeast enhanced green fluorescent protein-ubiquitin fusion protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GFL PDB ENTRY 1GFL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 1% Tryptone, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.34 47.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.515 α = 90 b = 65.649 β = 130.34 c = 70.225 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 100 CCD ADSC QUANTUM 210 mirrors 2009-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 1.4 100 99.1 0.058 22.3 3.7 62484 16.5
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) 1.4 1.42 100 0.545 2.58 3.6 3167
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1GFL 1.4 27.1 59297 3172 98.95 0.18022 0.1787 0.1757 0.20873 0.2059 RANDOM 21.07
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] -0.23 0.04 0.01 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.066 r_dihedral_angle_4_deg 15.438 r_dihedral_angle_3_deg 12.757 r_dihedral_angle_1_deg 6.842 r_scangle_it 4.955 r_scbond_it 3.062 r_mcangle_it 2.092 r_angle_refined_deg 1.884 r_mcbond_it 1.159 r_chiral_restr 0.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.066 r_dihedral_angle_4_deg 15.438 r_dihedral_angle_3_deg 12.757 r_dihedral_angle_1_deg 6.842 r_scangle_it 4.955 r_scbond_it 3.062 r_mcangle_it 2.092 r_angle_refined_deg 1.884 r_mcbond_it 1.159 r_chiral_restr 0.138 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2388 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 20
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling