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Crystal structure of siah2 SBD domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C9Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 25% PEG8000, 0.2 M NaCl, 0.1 M Hepes pH7.5
Crystal Properties Matthews coefficient Solvent content 2.22 44.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.624 α = 90 b = 68.753 β = 90 c = 102.884 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 ADSC QUANTUM 315 2015-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.76 50.01 100 0.101 0.106 0.034 7.2 9.2 38381
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.79 99.9 0.879 0.954 0.363 0.72 6.5 1894
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4C9Z 1.761 50.01 37374 945 99.7 0.17885 0.17761 0.22677 0.2195 RANDOM 21.803
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] -0.5 1.52 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.346 r_dihedral_angle_4_deg 17.869 r_dihedral_angle_3_deg 11.987 r_dihedral_angle_1_deg 6.318 r_long_range_B_refined 5.121 r_long_range_B_other 5.03 r_scangle_other 2.979 r_mcangle_it 2.224 r_mcangle_other 2.224 r_scbond_it 1.845
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.346 r_dihedral_angle_4_deg 17.869 r_dihedral_angle_3_deg 11.987 r_dihedral_angle_1_deg 6.318 r_long_range_B_refined 5.121 r_long_range_B_other 5.03 r_scangle_other 2.979 r_mcangle_it 2.224 r_mcangle_other 2.224 r_scbond_it 1.845 r_scbond_other 1.844 r_angle_refined_deg 1.506 r_mcbond_it 1.381 r_mcbond_other 1.379 r_angle_other_deg 0.932 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2935 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction MOLREP phasing ARP model building