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A new fluorescent protein darkmRuby at pH 9.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3U0M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 285 0.1 M CHES: NaOH pH 9.5, 30% (w/v) PEG3000
Crystal Properties Matthews coefficient Solvent content 2.6 52.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.54 α = 90 b = 76.93 β = 90.99 c = 66.65 γ = 90
Symmetry Space Group C 1 2 1
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 315r 2017-05-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 1.1158 ALS 12.3.1
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 2.8 45.89 99.4 0.994 9.1 4.71 13453
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 2.8 2.95 0.815
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 3u0m 2.8 45.89 12801 652 99.31 0.2004 0.197 0.1977 0.2708 0.268 RANDOM 46.169
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] 0.01 -0.14 0.18 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.886 r_dihedral_angle_4_deg 19.658 r_dihedral_angle_3_deg 18.52 r_dihedral_angle_1_deg 7.742 r_angle_refined_deg 1.583 r_angle_other_deg 1.246 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.886 r_dihedral_angle_4_deg 19.658 r_dihedral_angle_3_deg 18.52 r_dihedral_angle_1_deg 7.742 r_angle_refined_deg 1.583 r_angle_other_deg 1.246 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3489 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing