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Development of a family of redox-sensitive green fluorescent protein indicators for use in relatively oxidizing subcellular environments
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EMA PDB ENTRY 1EMA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1M tris, 22% PEG 1550, 0.02M magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2 38.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.066 α = 90 b = 62.701 β = 90 c = 70.136 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 210 2007-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.00 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.31 50 99.5 54553 52564 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.31 1.36 99.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 1EMA 1.31 30 2 51740 51740 2761 99.47 0.15341 0.15299 0.15212 0.1603 0.16922 0.1762 RANDOM 7.906
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] -0.03 -0.34 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.222 r_dihedral_angle_3_deg 10.351 r_dihedral_angle_4_deg 8.873 r_dihedral_angle_1_deg 6.18 r_sphericity_free 2.979 r_scangle_it 2.279 r_scbond_it 1.597 r_angle_refined_deg 1.372 r_rigid_bond_restr 1.338 r_sphericity_bonded 1.252
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.222 r_dihedral_angle_3_deg 10.351 r_dihedral_angle_4_deg 8.873 r_dihedral_angle_1_deg 6.18 r_sphericity_free 2.979 r_scangle_it 2.279 r_scbond_it 1.597 r_angle_refined_deg 1.372 r_rigid_bond_restr 1.338 r_sphericity_bonded 1.252 r_mcangle_it 1.16 r_angle_other_deg 0.785 r_mcbond_it 0.765 r_symmetry_vdw_other 0.326 r_mcbond_other 0.211 r_nbd_other 0.191 r_nbd_refined 0.187 r_nbtor_refined 0.167 r_symmetry_hbond_refined 0.129 r_nbtor_other 0.112 r_xyhbond_nbd_refined 0.102 r_symmetry_vdw_refined 0.085 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1843 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 2
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling