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Crystal Structure of the Monobody ySMB-1 bound to yeast SUMO
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FNA PDB ENTRIES 1FNA AND 2EKE experimental model PDB 2EKE PDB ENTRIES 1FNA AND 2EKE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 292 14% PEG8000, 16% glycerol, pH 8.0, VAPOR DIFFUSION, temperature 292K
Crystal Properties Matthews coefficient Solvent content 3.2 61.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.637 α = 90 b = 175.462 β = 90 c = 52.83 γ = 90
Symmetry Space Group P 21 21 2
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 225 mm CCD 2009-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F APS 21-ID-F
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 2.4 50 100 0.085 18.9 7.1 22586 22586
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 2.395 2.457 96.29 0.643 2.15 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 ENTRIES 1FNA AND 2EKE 2.4 20 21341 21341 1151 99.74 0.22558 0.22558 0.2231 0.27158 0.2705 RANDOM 49.816
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] -0.67 -0.03 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.575 r_dihedral_angle_3_deg 19.323 r_dihedral_angle_4_deg 18.328 r_dihedral_angle_1_deg 7.806 r_scangle_it 3.918 r_scbond_it 2.568 r_mcangle_it 1.923 r_angle_refined_deg 1.864 r_mcbond_it 1.107 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.575 r_dihedral_angle_3_deg 19.323 r_dihedral_angle_4_deg 18.328 r_dihedral_angle_1_deg 7.806 r_scangle_it 3.918 r_scbond_it 2.568 r_mcangle_it 1.923 r_angle_refined_deg 1.864 r_mcbond_it 1.107 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.27 r_nbd_refined 0.232 r_chiral_restr 0.16 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.14 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2666 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 48
Software Software Software Name Purpose MD2 data collection MAR345 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling