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Ribonuclease A in complex with adenosine-2',5'-diphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AFU PDB ENTRY 1AFU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 289 20mM Sodium citrate Buffer, 20% PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.67 25.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.852 α = 90 b = 32.528 β = 90.11 c = 72.383 γ = 90
Symmetry Space Group C 1 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 100 IMAGE PLATE MARRESEARCH Mirrors 2000-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.00061 ELETTRA 5.2R
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 1.2 30 92.1 0.038 30.9 14.1 67242 67242 0.01 -3 12.9
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) 1.2 1.22 71.2 0.226 2.8 2545
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1AFU 1.2 29.36 0.001 63814 63814 3421 92.9 0.19602 0.19431 0.19431 0.2012 0.22824 0.2335 RANDOM 14.68
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] -0.11 -0.05 0.31 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 12.842 r_dihedral_angle_1_deg 4.136 r_scangle_it 3.54 r_sphericity_bonded 2.701 r_sphericity_free 2.409 r_scbond_it 2.345 r_mcangle_it 1.927 r_angle_refined_deg 1.661 r_rigid_bond_restr 1.337 r_mcbond_it 1.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 12.842 r_dihedral_angle_1_deg 4.136 r_scangle_it 3.54 r_sphericity_bonded 2.701 r_sphericity_free 2.409 r_scbond_it 2.345 r_mcangle_it 1.927 r_angle_refined_deg 1.661 r_rigid_bond_restr 1.337 r_mcbond_it 1.233 r_angle_other_deg 0.863 r_symmetry_hbond_refined 0.295 r_symmetry_vdw_other 0.279 r_xyhbond_nbd_refined 0.269 r_nbd_refined 0.25 r_symmetry_vdw_refined 0.235 r_xyhbond_nbd_other 0.231 r_nbd_other 0.222 r_nbtor_other 0.191 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1902 Nucleic Acid Atoms Solvent Atoms 558 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling CNS phasing