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Crystal structure of a nanobody raised against KDM5B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EZJ 3EZJ chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 279 50mM Hepes, 150mM Nacl, 0,133 M NH4NO3 14% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.58 52.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.52 α = 90 b = 91.52 β = 90 c = 184.59 γ = 90
Symmetry Space Group P 43 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 110 CCD MAR CCD 165 mm 2014-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.85 41.21 100 0.11 0.11 0.118 0.043 12.2 7.5 67728 67728 20.15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.9 99.8 0.67 0.67 0.306 12.1 5.6 896
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 3EZJ chain A 1.85 41.206 1.36 67655 3308 99.95 0.1884 0.186 0.1875 0.2349 0.2354 Random Selection 27.013
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.148 f_angle_d 1.156 f_chiral_restr 0.042 f_bond_d 0.009 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5232 Nucleic Acid Atoms Solvent Atoms 730 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement SCALA data scaling PDB_EXTRACT data extraction PHASER phasing XDS data reduction