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Structure of the Red Fluorescent Protein mScarlet at pH 7.8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KCS pdbid 3KCS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 293 35-45% PEG 300, 100mM Sodium Phosphate Citrate
Crystal Properties Matthews coefficient Solvent content 2.44 49.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.2 α = 90 b = 35.64 β = 109.69 c = 86.01 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 PIXEL DECTRIS PILATUS 6M-F 2015-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.978 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.47 81 98.6 0.065 0.998 10.99 3.3 40759 -3 20.552
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.51 98.1 0.541 0.604 2.04
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 FREE R-VALUE pdbid 3KCS 1.47 80.98 38751 2008 98.67 0.1382 0.1368 0.1364 0.1669 0.1668 RANDOM 16.993
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] -0.42 0.02 0.22 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.097 r_sphericity_free 27.139 r_dihedral_angle_4_deg 17.285 r_dihedral_angle_3_deg 11.547 r_dihedral_angle_1_deg 6.492 r_sphericity_bonded 5.333 r_angle_refined_deg 1.643 r_rigid_bond_restr 1.481 r_mcangle_it 1.188 r_mcbond_it 1.033
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.097 r_sphericity_free 27.139 r_dihedral_angle_4_deg 17.285 r_dihedral_angle_3_deg 11.547 r_dihedral_angle_1_deg 6.492 r_sphericity_bonded 5.333 r_angle_refined_deg 1.643 r_rigid_bond_restr 1.481 r_mcangle_it 1.188 r_mcbond_it 1.033 r_mcbond_other 1.02 r_angle_other_deg 0.897 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1739 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 65
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction