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Bright-state structure of the reversibly switchable fluorescent protein Dronpa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A50 PDB ID 2A50
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 2.43 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.292 α = 90 b = 109.627 β = 90 c = 275.232 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 MAR CCD 165 mm 2005-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.04025 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 1.7 30 83.8 0.07 19.1 5.2 99209 104290 1 1 21
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 1.7 1.74 26.1 0.452 2.3 5.2 2333
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 ID 2A50 1.8 30 98948 5201 98.59 0.18678 0.18523 0.1833 0.21636 0.2138 RANDOM 29.716
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] 0.39 1.14 -1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.813 r_dihedral_angle_3_deg 14.641 r_dihedral_angle_4_deg 12.147 r_dihedral_angle_1_deg 6.573 r_scangle_it 2.647 r_scbond_it 1.752 r_angle_refined_deg 1.359 r_mcangle_it 1.017 r_mcbond_it 0.645 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.813 r_dihedral_angle_3_deg 14.641 r_dihedral_angle_4_deg 12.147 r_dihedral_angle_1_deg 6.573 r_scangle_it 2.647 r_scbond_it 1.752 r_angle_refined_deg 1.359 r_mcangle_it 1.017 r_mcbond_it 0.645 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.193 r_nbd_refined 0.188 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.095 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 7060 Nucleic Acid Atoms Solvent Atoms 883 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing