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Crystal structure of the Kelch domain of human KLHL12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DYH PDB ENTRY 2DYH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 0.2M AMMONIUM ACETATE, 0.1M SODIUM ACETATE PH4.6, 30% PEG4K
Crystal Properties Matthews coefficient Solvent content 1.77 30.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.637 α = 90 b = 61.546 β = 111.75 c = 45.523 γ = 90
Symmetry Space Group P 1 21 1
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 MARRESEARCH 2008-01-26 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 1.85 42.3 99.4 0.09 10.6 4.3 19527 23.09
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 1.85 1.95 96.1 0.63 2 3.4
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 PDB ENTRY 2DYH 1.85 42.3 18504 990 99.2 0.164 0.161 0.1693 0.222 0.2298 RANDOM 23.13
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] 0.21 -0.31 -1.58 1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.538 r_dihedral_angle_4_deg 18.535 r_dihedral_angle_3_deg 13.398 r_scangle_it 7.668 r_dihedral_angle_1_deg 7.581 r_scbond_it 5.868 r_mcangle_it 3.674 r_mcbond_it 2.429 r_angle_refined_deg 1.571 r_angle_other_deg 0.989
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.538 r_dihedral_angle_4_deg 18.535 r_dihedral_angle_3_deg 13.398 r_scangle_it 7.668 r_dihedral_angle_1_deg 7.581 r_scbond_it 5.868 r_mcangle_it 3.674 r_mcbond_it 2.429 r_angle_refined_deg 1.571 r_angle_other_deg 0.989 r_symmetry_vdw_other 0.298 r_nbd_other 0.249 r_nbd_refined 0.189 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.157 r_symmetry_vdw_refined 0.144 r_symmetry_hbond_refined 0.127 r_nbtor_other 0.119 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2184 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing