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Structure of HDAC like protein from Bordetella Alcaligenes bound the photoswitchable pyrazole Inhibitor CEW395
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G0X PDB ENTRY 5G0X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.25 pH 5.25
Crystal Properties Matthews coefficient Solvent content 2.87 57.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.099 α = 90 b = 101.099 β = 90 c = 175.057 γ = 90
Symmetry Space Group P 42 21 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 2015-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 1.81 31.45 99.9 0.14 15.4 20.6 82927 5.3
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 1.81 1.85 99.3 0.69 5.3 21
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 PDB ENTRY 5G0X 1.81 87.55 78680 4154 99.81 0.17335 0.17098 0.21853 0.2181 RANDOM 15.603
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] 0.02 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.477 r_dihedral_angle_4_deg 20.054 r_dihedral_angle_3_deg 12.287 r_dihedral_angle_1_deg 6.164 r_rigid_bond_restr 1.857 r_mcangle_it 1.639 r_angle_refined_deg 1.605 r_scbond_it 1.362 r_mcbond_it 1.36 r_mcbond_other 1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.477 r_dihedral_angle_4_deg 20.054 r_dihedral_angle_3_deg 12.287 r_dihedral_angle_1_deg 6.164 r_rigid_bond_restr 1.857 r_mcangle_it 1.639 r_angle_refined_deg 1.605 r_scbond_it 1.362 r_mcbond_it 1.36 r_mcbond_other 1.36 r_angle_other_deg 1.174 r_chiral_restr 0.123 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.004 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 r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5558 Nucleic Acid Atoms Solvent Atoms 989 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing