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Structure of an expanded Jab1-MPN-like domain of splicing factor Prp8p from yeast
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 2.5 % PEG 3350, 0.01 M CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.29 62.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.465 α = 90 b = 78.465 β = 90 c = 122.812 γ = 90
Symmetry Space Group P 42 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 MAR CCD 165 mm mirrors 2006-10-04 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MAR CCD 165 mm mirrors 2006-10-04 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 MPG/DESY, HAMBURG BW6 2 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 0.97890, 0.97920, 0.95000 MPG/DESY, HAMBURG BW6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 30 97.8 0.112 16.1 4.8 26671 26084 1 1 27.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 2 2.05 96 0.618 2.1 4.8 2003
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2 20 1 1 25289 24738 1315 97.82 0.20382 0.20176 0.2008 0.24149 0.2389 RANDOM 28.831
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] -1.42 -1.42 2.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.865 r_dihedral_angle_4_deg 18.013 r_dihedral_angle_3_deg 12.887 r_dihedral_angle_1_deg 5.961 r_scangle_it 2.364 r_scbond_it 1.444 r_mcangle_it 1.251 r_angle_refined_deg 1.186 r_mcbond_it 0.724 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.865 r_dihedral_angle_4_deg 18.013 r_dihedral_angle_3_deg 12.887 r_dihedral_angle_1_deg 5.961 r_scangle_it 2.364 r_scbond_it 1.444 r_mcangle_it 1.251 r_angle_refined_deg 1.186 r_mcbond_it 0.724 r_nbtor_refined 0.298 r_symmetry_vdw_refined 0.185 r_nbd_refined 0.182 r_xyhbond_nbd_refined 0.124 r_symmetry_hbond_refined 0.11 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1995 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling SHELXD phasing SHELXE model building