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Crystal structure of the third KH domain of FUBP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LIJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 10% PEG 6000, 10% ethylene glycol, 0.015M Zinkchlorid, 0.1 M MES, pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.36 47.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.409 α = 90 b = 47.409 β = 90 c = 147.893 γ = 120
Symmetry Space Group P 32 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 PILATUS3 2M 2018-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.918 BESSY 14.2
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 2 41.1 98.8 0.995 8.3 4.5 13595
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 2.05 0.661
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 4lij 2 41.09 12851 696 98.63 0.205 0.203 0.2118 0.2401 0.2398 RANDOM 35.66
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] -0.34 -0.17 -0.34 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.622 r_dihedral_angle_4_deg 16.072 r_dihedral_angle_3_deg 15.136 r_dihedral_angle_1_deg 6.241 r_angle_refined_deg 1.455 r_angle_other_deg 1.3 r_chiral_restr 0.077 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.622 r_dihedral_angle_4_deg 16.072 r_dihedral_angle_3_deg 15.136 r_dihedral_angle_1_deg 6.241 r_angle_refined_deg 1.455 r_angle_other_deg 1.3 r_chiral_restr 0.077 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1193 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 35
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing