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Crystal structure of Ang1-A451D receptor binding domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K0V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 4.0 M Sodium formate
Crystal Properties Matthews coefficient Solvent content 3.06 64.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.55 α = 90 b = 80.55 β = 90 c = 186.69 γ = 120
Symmetry Space Group P 64 2 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 2022-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9791 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.28 27.38 100 0.115 0.999 16.4 9.6 17164
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.32 1.239 0.765
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.28 27.38 16131 979 99.83 0.19909 0.1962 0.2066 0.24678 0.2484 RANDOM 44.362
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] 0.61 0.3 0.61 -1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.104 r_long_range_B_other 13.331 r_long_range_B_refined 13.327 r_scangle_other 9.024 r_dihedral_angle_1_deg 7.829 r_dihedral_angle_2_deg 6.94 r_mcangle_it 6.418 r_mcangle_other 6.417 r_scbond_it 5.99 r_scbond_other 5.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.104 r_long_range_B_other 13.331 r_long_range_B_refined 13.327 r_scangle_other 9.024 r_dihedral_angle_1_deg 7.829 r_dihedral_angle_2_deg 6.94 r_mcangle_it 6.418 r_mcangle_other 6.417 r_scbond_it 5.99 r_scbond_other 5.986 r_mcbond_it 4.401 r_mcbond_other 4.398 r_angle_refined_deg 1.696 r_angle_other_deg 0.64 r_chiral_restr 0.106 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 1760 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing