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Crystal structure of Danio rerio HDAC6 ZnF-UBP domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C5K PDB ENTRY 3C5K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 1M LI2SO4, 5M NICL2, 0.1M TRIS PH 8.5
Crystal Properties Matthews coefficient Solvent content 3.5 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.74 α = 90 b = 100.74 β = 90 c = 100.74 γ = 90
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 2M MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 50 95.8 0.13 6.85 2.9 12942 -3 25.27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 97.2 0.88 1.23 2.8
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 PDB ENTRY 3C5K 1.9 41.13 12942 641 95.35 0.1805 0.1787 0.1773 0.2147 0.2005 RANDOM 27.84
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 t_other_torsion 19 t_omega_torsion 3.73 t_angle_deg 0.97 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19 t_omega_torsion 3.73 t_angle_deg 0.97 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 859 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 14
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing