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Human Angiogenin mutant-S28A
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, SITTING DROP 289 Malic acid/NaOH pH 7.0, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.3 46.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.861 α = 90 b = 37.335 β = 90 c = 40.852 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 2019-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.8 83.86 93.9 0.999 21.1 3.3 11664
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 1.8 1.84 0.967
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 1.8 41.93 11014 618 93.44 0.20431 0.20145 0.25424 0.2621 RANDOM 39.883
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] -1.46 -4.35 5.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.408 r_dihedral_angle_4_deg 17.899 r_dihedral_angle_3_deg 14.996 r_long_range_B_other 10.961 r_long_range_B_refined 10.945 r_scangle_other 9.037 r_dihedral_angle_1_deg 6.643 r_scbond_it 6.423 r_scbond_other 6.419 r_mcangle_other 6.377
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.408 r_dihedral_angle_4_deg 17.899 r_dihedral_angle_3_deg 14.996 r_long_range_B_other 10.961 r_long_range_B_refined 10.945 r_scangle_other 9.037 r_dihedral_angle_1_deg 6.643 r_scbond_it 6.423 r_scbond_other 6.419 r_mcangle_other 6.377 r_mcangle_it 6.374 r_mcbond_it 4.966 r_mcbond_other 4.942 r_angle_refined_deg 1.498 r_angle_other_deg 1.093 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 975 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing