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Dark state structure of the reversibly switchable fluorescent protein Dronpa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IOV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 22% PEG 3350, 140mM Mg(NO3)2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 46.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.894 α = 90 b = 107.504 β = 90 c = 275.663 γ = 90
Symmetry Space Group I 2 2 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 CCD MARMOSAIC 225 mm CCD mirrors 2006-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.98 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.946 30 99.7 0.098 15.1 7.5 79713 79474
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.946 2.06 98.2 0.605 3 7.5
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 2IOV 1.946 30 75697 75485 3984 99.72 0.17621 0.17621 0.17407 0.1751 0.21612 0.2146 RANDOM 4.144
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] -0.11 -0.51 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.667 r_dihedral_angle_4_deg 19.808 r_dihedral_angle_3_deg 14.683 r_dihedral_angle_1_deg 6.683 r_scangle_it 2.55 r_scbond_it 1.579 r_angle_refined_deg 1.49 r_mcangle_it 0.645 r_mcbond_it 0.371 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.667 r_dihedral_angle_4_deg 19.808 r_dihedral_angle_3_deg 14.683 r_dihedral_angle_1_deg 6.683 r_scangle_it 2.55 r_scbond_it 1.579 r_angle_refined_deg 1.49 r_mcangle_it 0.645 r_mcbond_it 0.371 r_nbtor_refined 0.304 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.2 r_xyhbond_nbd_refined 0.169 r_symmetry_hbond_refined 0.145 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7024 Nucleic Acid Atoms Solvent Atoms 913 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling