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Crystal Structure of Ustilago sphaerogena Ribonuclease U2 complexed with adenosine 2'-monophosphate
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 hanging drop, vapor diffusion 6.5 293 PEG 8000, pH 6.5, hanging drop, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.994 α = 90 b = 35.94 β = 103.42 c = 36.151 γ = 90
Symmetry Space Group P 1 21 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 1.03 37.9 99.2 0.093 36.2 6.5 48243 47871 11.07
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) 1.03 1.057 93.9 0.395 2.2 3 3554
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 1.03 25.14 47871 2445 99.23 0.137 0.137 0.144 0.144 0.1478 RANDOM 10.729
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] 0.06 0.21 -0.01 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.075 r_dihedral_angle_3_deg 11.009 r_dihedral_angle_4_deg 7.816 r_dihedral_angle_1_deg 7.202 r_scangle_it 4.455 r_scbond_it 3.031 r_mcangle_it 2.269 r_angle_refined_deg 1.656 r_mcbond_it 1.5 r_rigid_bond_restr 1.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.075 r_dihedral_angle_3_deg 11.009 r_dihedral_angle_4_deg 7.816 r_dihedral_angle_1_deg 7.202 r_scangle_it 4.455 r_scbond_it 3.031 r_mcangle_it 2.269 r_angle_refined_deg 1.656 r_mcbond_it 1.5 r_rigid_bond_restr 1.155 r_angle_other_deg 0.927 r_mcbond_other 0.461 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.008 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 870 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing