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Human Angiogenin in complex with sulphate anions at an acidic solution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EOP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 289 0.1 M sodium cacodylate pH 6.0
2.0 M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.36 47.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.04 α = 90 b = 37.45 β = 90 c = 42.74 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 2015-09-13 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 2.4 42.9 100 0.138 9.3 5.5 5550
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 2.4 2.5 100 0.401 3.8 5.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5EOP 2.4 42.74 5226 298 99.95 0.18976 0.18632 0.1884 0.25005 0.2524 RANDOM 20.322
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] -0.96 -1.67 2.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.278 r_dihedral_angle_4_deg 20.053 r_dihedral_angle_3_deg 14.613 r_dihedral_angle_1_deg 6.637 r_long_range_B_refined 5.184 r_mcangle_it 2.34 r_scbond_it 1.673 r_angle_refined_deg 1.4 r_mcbond_it 1.324 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.278 r_dihedral_angle_4_deg 20.053 r_dihedral_angle_3_deg 14.613 r_dihedral_angle_1_deg 6.637 r_long_range_B_refined 5.184 r_mcangle_it 2.34 r_scbond_it 1.673 r_angle_refined_deg 1.4 r_mcbond_it 1.324 r_chiral_restr 0.096 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 974 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing