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Crystal Structure of Bovine Pancreatic Ribonuclease Complexed with Uridine-5'-monophosphate at 1.60 A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U1B PDB ENTRY 1U1B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 298 0.1 M HEPES BUFFER; Reservoir of 25% PEG3350 in water; droplets were 5-10 mM in basic fuchsin, tobramycin, uridine-5'-monophosphate and 1 mM in ribonuclease A, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.02 39.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.73 α = 90 b = 74.85 β = 107.8 c = 50.52 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 100 IMAGE PLATE RIGAKU RAXIS IV OSMIC MIRRORS 2007-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.6 29.54 91.2 0.027 16.8 2.61 25900 33.2
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 1.6 1.66 64.2 0.34 2.4 2.15
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1U1B 1.6 29.54 25900 23360 2540 90 0.203 0.197 0.2191 0.253 0.2774 RANDOM 38.71
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] 2.85 0.94 -1.64 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.458 r_dihedral_angle_3_deg 15.327 r_dihedral_angle_4_deg 12.911 r_scangle_it 7.017 r_dihedral_angle_1_deg 6.662 r_scbond_it 5.312 r_mcangle_it 4.409 r_mcbond_it 3.43 r_angle_refined_deg 1.549 r_mcbond_other 0.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.458 r_dihedral_angle_3_deg 15.327 r_dihedral_angle_4_deg 12.911 r_scangle_it 7.017 r_dihedral_angle_1_deg 6.662 r_scbond_it 5.312 r_mcangle_it 4.409 r_mcbond_it 3.43 r_angle_refined_deg 1.549 r_mcbond_other 0.925 r_angle_other_deg 0.689 r_symmetry_hbond_refined 0.234 r_nbd_refined 0.22 r_nbd_other 0.216 r_xyhbond_nbd_refined 0.209 r_symmetry_vdw_other 0.201 r_nbtor_refined 0.192 r_xyhbond_nbd_other 0.165 r_symmetry_vdw_refined 0.163 r_nbtor_other 0.096 r_chiral_restr 0.094 r_symmetry_hbond_other 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.001 r_bond_other_d r_metal_ion_refined r_metal_ion_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1902 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling