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Human angiogenin PD variant R95Q
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ANG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 0.2 M ammonium sulphate
0.1 M Na cacodylate
30% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.33 47.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.573 α = 90 b = 37.393 β = 90 c = 43.083 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 PIXEL DECTRIS PILATUS 6M-F 2016-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 82.6 96.6 0.998 11.1 12 29013
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.37 71.6 0.434 1.5 7 1033
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 1ANG 1.35 43.08 27556 1398 96.25 0.15209 0.15069 0.1594 0.1793 0.1874 RANDOM 20.03
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] -0.2 0.74 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.853 r_sphericity_free 27.634 r_dihedral_angle_4_deg 14.669 r_dihedral_angle_3_deg 14.063 r_sphericity_bonded 11.551 r_dihedral_angle_1_deg 6.608 r_long_range_B_refined 3.982 r_long_range_B_other 3.685 r_scangle_other 3.297 r_scbond_it 2.749
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.853 r_sphericity_free 27.634 r_dihedral_angle_4_deg 14.669 r_dihedral_angle_3_deg 14.063 r_sphericity_bonded 11.551 r_dihedral_angle_1_deg 6.608 r_long_range_B_refined 3.982 r_long_range_B_other 3.685 r_scangle_other 3.297 r_scbond_it 2.749 r_scbond_other 2.746 r_rigid_bond_restr 2.665 r_mcangle_other 2.234 r_mcangle_it 2.229 r_angle_refined_deg 1.75 r_mcbond_it 1.736 r_mcbond_other 1.683 r_angle_other_deg 1.045 r_chiral_restr 0.102 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 980 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing