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Crystal structure of Siah1 at 1.95 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A25 PDB ENTRY 2A25
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 MES PH6.5, 1.5 M MGSO4).
Crystal Properties Matthews coefficient Solvent content 2.99 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.14 α = 90 b = 104.59 β = 90 c = 133.16 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 IMAGE PLATE RIGAKU RAXIS IV 2011-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 1.95 44.99 99.3 0.04 19.3 3.7 38340 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 1.95 2.06 96 0.18 4.5 2.1
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 PDB ENTRY 2A25 1.95 40 36417 1918 99.27 0.19967 0.19761 0.23855 0.2613 RANDOM 42.28
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] -0.2 0.55 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.793 r_dihedral_angle_3_deg 15.277 r_dihedral_angle_4_deg 10.572 r_scangle_it 7.837 r_scbond_it 5.572 r_dihedral_angle_1_deg 5.568 r_mcangle_it 3.539 r_mcbond_it 2.345 r_angle_refined_deg 1.302 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.793 r_dihedral_angle_3_deg 15.277 r_dihedral_angle_4_deg 10.572 r_scangle_it 7.837 r_scbond_it 5.572 r_dihedral_angle_1_deg 5.568 r_mcangle_it 3.539 r_mcbond_it 2.345 r_angle_refined_deg 1.302 r_chiral_restr 0.093 r_bond_refined_d 0.011 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_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 3002 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing