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Crystal structure of human Angiogenin at 1.35 Angstroms resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B1I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 289 Malic acid/NaOH pH 7.0
PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.9 35.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.664 α = 90 b = 37.559 β = 90 c = 33.012 γ = 90
Symmetry Space Group P 21 21 2
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 MARMOSAIC 225 mm CCD 2015-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.0403 MAX II I911-3
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 1.35 42.83 98.7 0.057 12.7 4.8 23977
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 1.35 1.37 99 0.481 3 4.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1B1I 1.35 42.83 22728 1222 98.47 0.14968 0.1474 0.19155 0.2004 RANDOM 18.766
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] -0.29 -0.02 0.32
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.367 r_dihedral_angle_2_deg 27.109 r_dihedral_angle_4_deg 18.759 r_dihedral_angle_3_deg 11.697 r_sphericity_bonded 9.781 r_dihedral_angle_1_deg 6.695 r_long_range_B_refined 4.073 r_long_range_B_other 3.692 r_scangle_other 2.725 r_mcangle_it 2.398
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.367 r_dihedral_angle_2_deg 27.109 r_dihedral_angle_4_deg 18.759 r_dihedral_angle_3_deg 11.697 r_sphericity_bonded 9.781 r_dihedral_angle_1_deg 6.695 r_long_range_B_refined 4.073 r_long_range_B_other 3.692 r_scangle_other 2.725 r_mcangle_it 2.398 r_mcangle_other 2.398 r_rigid_bond_restr 2.327 r_scbond_it 2.187 r_scbond_other 2.185 r_angle_refined_deg 1.892 r_mcbond_it 1.768 r_mcbond_other 1.757 r_angle_other_deg 1.124 r_chiral_restr 0.119 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 976 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing