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Crystal structure of Siah1 at 1.58 A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C9Z PDB ENTRY 4C9Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 CRYSTALS GREW FROM EQUAL VOLUMES OF PROTEIN SOLUTION (15 MG ML-1 IN 15 MM TRIS-HCL PH7.5, 30 MM NACL AND 10 MM DTT) AND RESERVOIR SOLUTION (100 MM HEPES PH7.0, 1.45 LI2SO4).
Crystal Properties Matthews coefficient Solvent content 2.99 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.06 α = 90 b = 104.12 β = 90 c = 133.59 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 287 PIXEL DECTRIS PILATUS 6M 2012-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.58 52.06 100 0.05 16.1 4.9 72738 2
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 1.58 1.67 100 0.48 3.5 4.8
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 4C9Z 1.58 52.11 69071 3666 99.95 0.14315 0.14075 0.1698 0.18907 0.1984 RANDOM 30.821
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] -0.23 -0.73 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.065 r_sphericity_free 30.633 r_dihedral_angle_4_deg 22.873 r_sphericity_bonded 22.131 r_dihedral_angle_3_deg 15.895 r_rigid_bond_restr 10.043 r_dihedral_angle_1_deg 6.345 r_angle_refined_deg 2.335 r_chiral_restr 0.171 r_bond_refined_d 0.023
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.065 r_sphericity_free 30.633 r_dihedral_angle_4_deg 22.873 r_sphericity_bonded 22.131 r_dihedral_angle_3_deg 15.895 r_rigid_bond_restr 10.043 r_dihedral_angle_1_deg 6.345 r_angle_refined_deg 2.335 r_chiral_restr 0.171 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2975 Nucleic Acid Atoms Solvent Atoms 331 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing