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Crystal structure of human SMURF1 C2 domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M HEPES (pH 6.5), 2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.24 45.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.959 α = 90 b = 47.048 β = 90 c = 91.266 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 315r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.96 50 99.6 10154 10113 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.96 32.76 9586 485 99.61 0.20582 0.20413 0.2012 0.24115 0.2445 RANDOM 23.774
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] 2.51 -1.12 -1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.207 r_dihedral_angle_3_deg 17.531 r_dihedral_angle_4_deg 13.537 r_dihedral_angle_1_deg 6.807 r_scangle_it 5.332 r_scbond_it 3.352 r_mcangle_it 2.054 r_angle_refined_deg 1.7 r_mcbond_it 1.25 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.207 r_dihedral_angle_3_deg 17.531 r_dihedral_angle_4_deg 13.537 r_dihedral_angle_1_deg 6.807 r_scangle_it 5.332 r_scbond_it 3.352 r_mcangle_it 2.054 r_angle_refined_deg 1.7 r_mcbond_it 1.25 r_nbtor_refined 0.311 r_nbd_refined 0.235 r_symmetry_vdw_refined 0.213 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.14 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1038 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 11
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling