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Crystal structure of monomeric near-infrared fluorescent protein miRFP709
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XTQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.16 M MgCl2, 0.08 M Tris-HCl pH 8.5, 20% w/v PEG 3350, 3.2% 2,2,2-trifluoroethanol
Crystal Properties Matthews coefficient Solvent content 1.79 31.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.266 α = 90 b = 52.86 β = 92.7 c = 64.625 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 225 mm CCD 2016-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.34 27.54 99.6 0.055 0.065 0.033 15.4 3.6 55190
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.34 1.39 97.6 0.517 0.62 0.336 0.829 3.2
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 4XTQ 1.34 27.54 53465 1701 99.37 0.1373 0.1357 0.1362 0.1877 0.1878 RANDOM 23.532
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] 1.57 -2.43 -1.28 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.648 r_sphericity_free 21.01 r_dihedral_angle_4_deg 20.151 r_dihedral_angle_3_deg 14.799 r_sphericity_bonded 13.257 r_rigid_bond_restr 8.78 r_dihedral_angle_1_deg 6.78 r_angle_refined_deg 2.348 r_angle_other_deg 1.509 r_chiral_restr 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.648 r_sphericity_free 21.01 r_dihedral_angle_4_deg 20.151 r_dihedral_angle_3_deg 14.799 r_sphericity_bonded 13.257 r_rigid_bond_restr 8.78 r_dihedral_angle_1_deg 6.78 r_angle_refined_deg 2.348 r_angle_other_deg 1.509 r_chiral_restr 0.136 r_bond_refined_d 0.023 r_gen_planes_other 0.016 r_gen_planes_refined 0.014 r_bond_other_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2303 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 43
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction MOLREP phasing