☰ Navigation Tabs
Bovine Seminal Ribonuclease- cytidine 5' phosphate complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R5D PDB ENTRY 1R5D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 30% PEG4000, 0.1M sodium acetate, 0.1M Tris/HCl, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.16 43.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.585 α = 90 b = 59.016 β = 90 c = 82.247 γ = 90
Symmetry Space Group P 21 21 21
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 2007-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8088 EMBL/DESY, HAMBURG X13
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 1.69 27.775 98.1 0.059 14.1 3.9 26589 26554 -3 16.968
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 1.7 1.73 98.7 0.445 3.4 3.8 4382
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1R5D 1.69 27.77 25228 1326 97.45 0.17036 0.16862 0.1676 0.20428 0.2036 RANDOM 14.364
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] -0.07 -0.1 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.825 r_dihedral_angle_3_deg 12.498 r_dihedral_angle_4_deg 11.941 r_dihedral_angle_1_deg 5.844 r_scangle_it 2.907 r_scbond_it 1.862 r_angle_refined_deg 1.284 r_mcangle_it 1.14 r_mcbond_it 0.685 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.825 r_dihedral_angle_3_deg 12.498 r_dihedral_angle_4_deg 11.941 r_dihedral_angle_1_deg 5.844 r_scangle_it 2.907 r_scbond_it 1.862 r_angle_refined_deg 1.284 r_mcangle_it 1.14 r_mcbond_it 0.685 r_nbtor_refined 0.293 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.157 r_symmetry_hbond_refined 0.137 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1882 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling REFMAC phasing