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X-ray crystal structure of the N-terminal BTB domain of human KCTD5 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DRX PDB entry 3DRX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 298 24% (w/v) PEG 3350, 100 mM MgCl2, 100 M HEPES, pH 7.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.41 48.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.039 α = 90 b = 90.718 β = 90 c = 110.158 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD ADJUSTABLE FOCUSING MIRRORS
K-B GEOMETRY 2006-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97934 APS 23-ID-D
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 99.7 0.065 21.15 4 46924
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 99.4 0.412 3.32 4 3090
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3DRX 1.9 20 44550 44550 2374 99.65 0.19548 0.19548 0.19357 0.23226 0.262 RANDOM 40.152
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] -0.46 -2.62 3.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.715 r_dihedral_angle_4_deg 21.825 r_dihedral_angle_3_deg 13.856 r_dihedral_angle_1_deg 4.672 r_scangle_it 3.814 r_scbond_it 2.396 r_mcangle_it 1.677 r_angle_refined_deg 1.196 r_mcbond_it 0.938 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.715 r_dihedral_angle_4_deg 21.825 r_dihedral_angle_3_deg 13.856 r_dihedral_angle_1_deg 4.672 r_scangle_it 3.814 r_scbond_it 2.396 r_mcangle_it 1.677 r_angle_refined_deg 1.196 r_mcbond_it 0.938 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4066 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing