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Human angiogenin ALS variant V103I
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, HANGING DROP 6.5 289 0.2 M Na/K tartrate
0.1 M MES
20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.12 60.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.749 α = 90 b = 115.906 β = 90 c = 37.288 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS 6M 2012-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 1.85 67.4 90.7 0.993 6.3 6.5 14125
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 1.85 1.89 76.3 0.461 1 2.8 723
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 1ANG 1.85 67.35 13073 1042 89.47 0.21218 0.20824 0.26447 0.2573 RANDOM 33.444
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] -1.63 4.51 -2.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.673 r_dihedral_angle_3_deg 14.31 r_dihedral_angle_4_deg 14.114 r_long_range_B_refined 7.095 r_long_range_B_other 6.987 r_dihedral_angle_1_deg 6.896 r_scangle_other 4.803 r_mcangle_it 3.611 r_mcangle_other 3.611 r_scbond_it 2.929
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.673 r_dihedral_angle_3_deg 14.31 r_dihedral_angle_4_deg 14.114 r_long_range_B_refined 7.095 r_long_range_B_other 6.987 r_dihedral_angle_1_deg 6.896 r_scangle_other 4.803 r_mcangle_it 3.611 r_mcangle_other 3.611 r_scbond_it 2.929 r_scbond_other 2.903 r_mcbond_it 2.217 r_mcbond_other 2.211 r_angle_refined_deg 1.492 r_angle_other_deg 0.943 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 966 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing