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Crystal structure of an Anticalin directed towards colchicine without ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NKN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 PEG 3350, calcium chloride
Crystal Properties Matthews coefficient Solvent content 1.97 37.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.557 α = 90 b = 75.579 β = 90 c = 116.12 γ = 90
Symmetry Space Group I 2 2 2
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 PILATUS3 S 6M Si mirror 2019-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91840 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.779 63.343 99.6 0.06 0.064 0.019 17.6 10.5 16656 16656
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.88 99.8 0.418 0.418 0.438 0.129 1.8 11.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5NKN 1.78 63.34 15844 811 99.35 0.2036 0.2007 0.2585 0.2749 RANDOM 42.129
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] 1.97 0.1 -2.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.412 r_dihedral_angle_3_deg 15.977 r_dihedral_angle_4_deg 10.974 r_dihedral_angle_1_deg 7.669 r_angle_refined_deg 1.375 r_angle_other_deg 1.234 r_chiral_restr 0.055 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.412 r_dihedral_angle_3_deg 15.977 r_dihedral_angle_4_deg 10.974 r_dihedral_angle_1_deg 7.669 r_angle_refined_deg 1.375 r_angle_other_deg 1.234 r_chiral_restr 0.055 r_bond_refined_d 0.007 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 1393 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 1
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction