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A degradation product of PD 404182 (P2742) bound to Histone Deacetylase-like Amidohydrolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.25 293 0.1 M Malate-Imidazole buffer pH 5.25, 4 % PEG400
Crystal Properties Matthews coefficient Solvent content 2.78 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.68 α = 90 b = 100.68 β = 90 c = 175.53 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 2015-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99988 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.47 87.77 100 0.146 0.06 0.996 10.6 13.1 152110
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.5 0.409 0.791
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 5G1A 1.47 87.77 144560 7459 99.94 0.14591 0.14442 0.1446 0.17446 0.1747 RANDOM 16.193
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 0.34 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.494 r_sphericity_free 28.362 r_dihedral_angle_4_deg 16.825 r_dihedral_angle_3_deg 10.767 r_sphericity_bonded 10.37 r_dihedral_angle_1_deg 6.087 r_long_range_B_refined 3.819 r_long_range_B_other 3.586 r_scangle_other 2.727 r_scbond_it 2.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.494 r_sphericity_free 28.362 r_dihedral_angle_4_deg 16.825 r_dihedral_angle_3_deg 10.767 r_sphericity_bonded 10.37 r_dihedral_angle_1_deg 6.087 r_long_range_B_refined 3.819 r_long_range_B_other 3.586 r_scangle_other 2.727 r_scbond_it 2.305 r_scbond_other 2.305 r_mcangle_it 2.008 r_mcangle_other 2.008 r_rigid_bond_restr 1.695 r_mcbond_it 1.573 r_mcbond_other 1.57 r_angle_refined_deg 1.462 r_angle_other_deg 0.97 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5533 Nucleic Acid Atoms Solvent Atoms 830 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing