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Structural and spectroscopic characterization of photoconverting fluorescent protein Dendra2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZUX PDB ENTRY 1ZUX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.8 32% PEG 3350, 0.1M MAGNESIUM NITRATE, PH 8.8
Crystal Properties Matthews coefficient Solvent content 2.07 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.26 α = 90.05 b = 76.85 β = 108.17 c = 92.5 γ = 106.58
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 CCD TOROIDAL FOCUSING MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2 33.5 94.1 0.05 12.15 1.95 113215 25.5
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 2 2.1 94.5 0.17 4.42 1.85
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 1ZUX 2 33.5 107552 5661 100 0.21517 0.21229 0.2113 0.2689 0.269 RANDOM 21.816
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.272 r_dihedral_angle_4_deg 18.46 r_dihedral_angle_3_deg 14.277 r_dihedral_angle_1_deg 6.898 r_scangle_it 2.268 r_angle_refined_deg 1.415 r_scbond_it 1.41 r_mcangle_it 0.939 r_mcbond_it 0.518 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.272 r_dihedral_angle_4_deg 18.46 r_dihedral_angle_3_deg 14.277 r_dihedral_angle_1_deg 6.898 r_scangle_it 2.268 r_angle_refined_deg 1.415 r_scbond_it 1.41 r_mcangle_it 0.939 r_mcbond_it 0.518 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14474 Nucleic Acid Atoms Solvent Atoms 1280 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing