☰ Navigation Tabs
A new fluorescent protein darkmRuby at pH 5.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3U0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 285 0.2 M lithium sulfate, 0.1 M sodium acetate: acetic acid pH 4.5, 30% (w/v) PEG8000
Crystal Properties Matthews coefficient Solvent content 2.38 48.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.571 α = 90 b = 101.685 β = 90 c = 134.983 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS 6M 2019-06-20 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9795 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.8 47.62 100 0.997 10.4 7.36 47367
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 99.9 0.842
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 3u0l 1.8 47.58 44943 2366 99.81 0.1773 0.1756 0.186 0.2106 0.22 RANDOM 22.209
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] -1.26 -0.54 1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.437 r_dihedral_angle_4_deg 16.415 r_dihedral_angle_3_deg 13.857 r_dihedral_angle_1_deg 7.103 r_angle_refined_deg 1.569 r_angle_other_deg 1.326 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.437 r_dihedral_angle_4_deg 16.415 r_dihedral_angle_3_deg 13.857 r_dihedral_angle_1_deg 7.103 r_angle_refined_deg 1.569 r_angle_other_deg 1.326 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3502 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing