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Crystal Structure of Ustilago sphaerogena Ribonuclease U2 complexed with adenosine 3'-monophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RTU PDB ENTRY 1RTU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.75 293 12.5% PEG 8000, 200mM calcium acetate, 100mM sodium cacodylate, 240mM HCl, pH 3.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.6464 25.2916
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.586 α = 90 b = 39.425 β = 108.98 c = 31.646 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 2010-01-01 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 0.99 34.3 96.2 0.061 58 9.2 43053 9.8
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 0.99 1.02 92.4 0.433 6.6 6.7 3011
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 1RTU 0.99 32.71 40857 2196 96.04 0.151 0.15 0.1525 0.162 0.1655 RANDOM 9.168
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] 0.52 0.14 -1 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.358 r_dihedral_angle_4_deg 17.894 r_dihedral_angle_3_deg 11.827 r_dihedral_angle_1_deg 7.373 r_scangle_it 4.03 r_angle_other_deg 3.524 r_scbond_it 2.848 r_mcangle_it 2.166 r_angle_refined_deg 1.9 r_mcbond_it 1.411
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.358 r_dihedral_angle_4_deg 17.894 r_dihedral_angle_3_deg 11.827 r_dihedral_angle_1_deg 7.373 r_scangle_it 4.03 r_angle_other_deg 3.524 r_scbond_it 2.848 r_mcangle_it 2.166 r_angle_refined_deg 1.9 r_mcbond_it 1.411 r_rigid_bond_restr 1.118 r_mcbond_other 0.412 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 870 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing