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Structure of HDAC like protein from Bordetella Alcaligenes in complex with the photoswitchable inhibitor CEW65
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZZ0 PDB ENTRY 1ZZ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.25 PEG 400 MALATE IMIDAZOLE PH 5.25
Crystal Properties Matthews coefficient Solvent content 2.42 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.27 α = 90 b = 130.14 β = 90 c = 251.13 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 PILATUS 6M 2015-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 1.6 20.67 99.7 0.1 9.1 5.6 197317 2.9
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 1.6 1.63 99.8 0.46 2.9 5.5
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 1ZZ0 1.6 125.57 187354 9836 99.6 0.12701 0.12496 0.1394 0.16662 0.176 RANDOM 15.601
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] -0.23 0.73 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.351 r_sphericity_free 34.384 r_dihedral_angle_4_deg 17.835 r_dihedral_angle_3_deg 11.406 r_sphericity_bonded 8.848 r_dihedral_angle_1_deg 6.241 r_rigid_bond_restr 1.985 r_mcangle_it 1.772 r_scbond_it 1.73 r_angle_refined_deg 1.538
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.351 r_sphericity_free 34.384 r_dihedral_angle_4_deg 17.835 r_dihedral_angle_3_deg 11.406 r_sphericity_bonded 8.848 r_dihedral_angle_1_deg 6.241 r_rigid_bond_restr 1.985 r_mcangle_it 1.772 r_scbond_it 1.73 r_angle_refined_deg 1.538 r_mcbond_it 1.373 r_mcbond_other 1.373 r_angle_other_deg 1.001 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11096 Nucleic Acid Atoms Solvent Atoms 1791 Heterogen Atoms 201
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling