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Crystal Structure of Ustilago sphaerogena Ribonuclease U2B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AGN PDB ENTRY 3AGN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 293 0.84M sodium dihydrogenphosphate, 1.26M dipotassium hydrogenphosphate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.28 62.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.237 α = 90 b = 98.237 β = 90 c = 87.605 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 4r 2010-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.978 Photon Factory BL-6A
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 1.32 50 99.98 0.081 68.5 15 114464 114464 -3 20
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 1.32 1.37 99.9 0.587 4 10 8374
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 3AGN 1.32 50 114132 5706 99.71 0.163 0.162 0.1657 0.174 0.1785 RANDOM 17.127
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] 0.14 0.07 0.14 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.445 r_dihedral_angle_3_deg 11.209 r_dihedral_angle_4_deg 8.932 r_dihedral_angle_1_deg 6.623 r_angle_other_deg 5.263 r_scangle_it 4.401 r_mcbond_other 3.221 r_scbond_it 3.061 r_mcangle_it 2.322 r_rigid_bond_restr 2.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.445 r_dihedral_angle_3_deg 11.209 r_dihedral_angle_4_deg 8.932 r_dihedral_angle_1_deg 6.623 r_angle_other_deg 5.263 r_scangle_it 4.401 r_mcbond_other 3.221 r_scbond_it 3.061 r_mcangle_it 2.322 r_rigid_bond_restr 2.135 r_angle_refined_deg 1.487 r_mcbond_it 1.428 r_chiral_restr 0.082 r_gen_planes_other 0.013 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2570 Nucleic Acid Atoms Solvent Atoms 404 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing