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X-ray crystal structure of human KCTD5 protein crystallized in low-salt buffer
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 0.2 M proline, 100 mM HEPES, 7% (w/v) PEG 3350, pH 7.5, VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 2.63 53.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.99 α = 90 b = 106.791 β = 90 c = 110.174 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 0.97915 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 3.3 50 99.5 0.074 18.14 5.2 20180
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 3.3 3.4 97.6 0.51 1.9 4.8 1151
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 (All) 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 3DRX 3.3 20 16774 1913 99.7 0.26018 0.26018 0.25257 0.2658 0.30791 0.3369 RANDOM 73.224
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] -8.94 -4.73 13.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.47 r_dihedral_angle_3_deg 19.233 r_dihedral_angle_4_deg 17.817 r_dihedral_angle_1_deg 6.843 r_angle_refined_deg 1.276 r_angle_other_deg 0.941 r_scangle_it 0.743 r_scbond_it 0.478 r_mcangle_it 0.428 r_mcbond_it 0.373
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.47 r_dihedral_angle_3_deg 19.233 r_dihedral_angle_4_deg 17.817 r_dihedral_angle_1_deg 6.843 r_angle_refined_deg 1.276 r_angle_other_deg 0.941 r_scangle_it 0.743 r_scbond_it 0.478 r_mcangle_it 0.428 r_mcbond_it 0.373 r_nbd_refined 0.232 r_symmetry_vdw_other 0.213 r_symmetry_hbond_refined 0.21 r_symmetry_vdw_refined 0.196 r_nbd_other 0.19 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.166 r_nbtor_other 0.087 r_xyhbond_nbd_other 0.07 r_chiral_restr 0.066 r_mcbond_other 0.051 r_bond_refined_d 0.012 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6810 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing