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Crystal structure of a HDAC-like protein with acetate bound
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 NaK-phosphate, Na-acetate, 1,4-butanediol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.586 α = 90 b = 127.886 β = 90 c = 251.681 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 99
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.6 44.86 188375 10000 99.63 0.16353 0.16232 0.1622 0.18587 0.1853 RANDOM 17.281
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 r_dihedral_angle_2_deg 37.641 r_dihedral_angle_4_deg 16.347 r_dihedral_angle_3_deg 11.573 r_dihedral_angle_1_deg 5.963 r_scangle_it 3.746 r_scbond_it 2.506 r_angle_refined_deg 1.474 r_mcangle_it 1.363 r_mcbond_it 0.786 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.641 r_dihedral_angle_4_deg 16.347 r_dihedral_angle_3_deg 11.573 r_dihedral_angle_1_deg 5.963 r_scangle_it 3.746 r_scbond_it 2.506 r_angle_refined_deg 1.474 r_mcangle_it 1.363 r_mcbond_it 0.786 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.236 r_nbd_refined 0.222 r_symmetry_hbond_refined 0.201 r_xyhbond_nbd_refined 0.144 r_metal_ion_refined 0.135 r_chiral_restr 0.101 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10988 Nucleic Acid Atoms Solvent Atoms 1235 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CCP4 phasing