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3.0 angstrom resolution structure of a Y22M mutant of the spliceosomal protein p14 bound to a region of SF3b155
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F9D pdbid 2f9d
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 60% NaH2PO4/40% K2HPO4
0.5M beta-alanine, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.41 63.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.271 α = 90 b = 71.271 β = 90 c = 102.284 γ = 90
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 210 2005-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
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 3 100 99.8 0.059 4.2 10288
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 3 3.11 100 0.46 4.2
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 pdbid 2f9d 3 71.25 9775 488 99.83 0.22128 0.21906 0.215 0.26586 0.2609 RANDOM 79.734
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] 2.59 2.59 -5.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.67 r_dihedral_angle_3_deg 22.17 r_dihedral_angle_4_deg 17.401 r_dihedral_angle_1_deg 6.113 r_scangle_it 1.57 r_angle_refined_deg 1.328 r_scbond_it 1.009 r_mcangle_it 0.87 r_mcbond_it 0.486 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.67 r_dihedral_angle_3_deg 22.17 r_dihedral_angle_4_deg 17.401 r_dihedral_angle_1_deg 6.113 r_scangle_it 1.57 r_angle_refined_deg 1.328 r_scbond_it 1.009 r_mcangle_it 0.87 r_mcbond_it 0.486 r_nbtor_refined 0.311 r_nbd_refined 0.228 r_symmetry_hbond_refined 0.191 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.099 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 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 2417 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction