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Crystal structure of the UHM domain of human SPF45 in complex with SF3b155-ULM5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PE8 PDB-ID 2pe8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 25% (w/v) PEG 1,500, 0.1 M Malonate, Imidazole, Borate buffer pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 42.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.92 α = 90 b = 66.38 β = 90 c = 72.77 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2006-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.05 38.3 89.3 0.049 0.045 32.56 7.1 13008 13008 -3 -3 22
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.17 78.5 0.206 0.188 9.46 6.75 1819
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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-ID 2pe8 2.11 38.84 -3 -3 11550 11550 613 91.63 0.21132 0.21132 0.20811 0.2122 0.27272 0.277 RANDOM 21.339
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] -0.87 0.52 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.565 r_dihedral_angle_4_deg 18.328 r_dihedral_angle_3_deg 15.222 r_dihedral_angle_1_deg 5.632 r_scangle_it 2.148 r_scbond_it 1.51 r_angle_refined_deg 1.385 r_angle_other_deg 1.177 r_mcangle_it 0.847 r_mcbond_it 0.731
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.565 r_dihedral_angle_4_deg 18.328 r_dihedral_angle_3_deg 15.222 r_dihedral_angle_1_deg 5.632 r_scangle_it 2.148 r_scbond_it 1.51 r_angle_refined_deg 1.385 r_angle_other_deg 1.177 r_mcangle_it 0.847 r_mcbond_it 0.731 r_symmetry_vdw_refined 0.351 r_symmetry_hbond_refined 0.216 r_nbd_other 0.194 r_nbd_refined 0.192 r_nbtor_refined 0.172 r_symmetry_vdw_other 0.155 r_chiral_restr 0.153 r_mcbond_other 0.134 r_xyhbond_nbd_refined 0.129 r_nbtor_other 0.083 r_bond_refined_d 0.013 r_bond_other_d 0.006 r_xyhbond_nbd_other 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1760 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection XDS data reduction XDS data scaling PHASER phasing