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X-ray structure of Cerulean GFP: A tryptophan-based chromophore useful for fluorescence lifetime imaging
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OXD PDB ENTRY 1OXD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277 100mM sodium acetate, 19% PEG 4000, 1mM EDTA, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.973337 37.669037
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.232 α = 90 b = 63.339 β = 90 c = 69.821 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 100 CCD ADSC QUANTUM 315 2006-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0000 ALS 5.0.2
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 2 20 99.5 0.082 0.082 5.1 5.7 15852 4 14.95
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 2 2.11 99.4 0.207 0.207 1.8 5.8 13288
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 1OXD 2 19.92 15023 791 99.47 0.19172 0.18806 0.1882 0.26206 0.2628 RANDOM 13.245
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] -0.38 -0.23 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.203 r_dihedral_angle_4_deg 16.214 r_dihedral_angle_3_deg 14.669 r_dihedral_angle_1_deg 7.056 r_scangle_it 4.824 r_scbond_it 3.02 r_angle_refined_deg 1.866 r_mcangle_it 1.789 r_mcbond_it 1.155 r_symmetry_hbond_refined 0.339
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.203 r_dihedral_angle_4_deg 16.214 r_dihedral_angle_3_deg 14.669 r_dihedral_angle_1_deg 7.056 r_scangle_it 4.824 r_scbond_it 3.02 r_angle_refined_deg 1.866 r_mcangle_it 1.789 r_mcbond_it 1.155 r_symmetry_hbond_refined 0.339 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.113 r_bond_refined_d 0.017 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1789 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ALS data collection MOSFLM data reduction SCALA data scaling MOLREP phasing