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Crystal structure of human cleavage and polyadenylation specificity factor 5 (CPSF5) in complex with a sulphate ion.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CL3 PDB ENTRY 2CL3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 17%(W/V)PEG3350, 0.2M AMSO4, 0.1M BIS TRIS PH 5.2.MIX 1:1UL DROPS OF 9MG/ML PROTEIN WITH WELL SOLUTION IN RT THEN MOVE TO CR.
Crystal Properties Matthews coefficient Solvent content 2.72 54.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.4 α = 90 b = 86.4 β = 90 c = 139.7 γ = 90
Symmetry Space Group P 41 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 110 CCD ADSC CCD 2006-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.3 25 99.1 0.1 13.6 6 24012 -3
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 2.3 2.5 98.3 0.32 3.94 5.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2CL3 2.3 25 22810 1201 99.2 0.22 0.218 0.2103 0.269 0.2611 RANDOM 35
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] 1.41 1.41 -2.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.106 r_dihedral_angle_4_deg 17.305 r_dihedral_angle_3_deg 15.64 r_dihedral_angle_1_deg 6.915 r_scangle_it 1.698 r_angle_refined_deg 1.3 r_scbond_it 1.081 r_mcangle_it 0.81 r_mcbond_it 0.463 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.106 r_dihedral_angle_4_deg 17.305 r_dihedral_angle_3_deg 15.64 r_dihedral_angle_1_deg 6.915 r_scangle_it 1.698 r_angle_refined_deg 1.3 r_scbond_it 1.081 r_mcangle_it 0.81 r_mcbond_it 0.463 r_nbtor_refined 0.304 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.173 r_symmetry_hbond_refined 0.154 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.104 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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_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 3280 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing