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Crystal structure of Ang1 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 3.5 M Sodium formate at pH 7.0
Crystal Properties Matthews coefficient Solvent content 1.85 38.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.6 α = 90 b = 61.98 β = 100.59 c = 44.55 γ = 90
Symmetry Space Group C 1 2 1
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 PILATUS3 6M 2021-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 1.0 SSRF BL19U1
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 1.75 24.05 99.8 0.11 0.998 10.7 6.7 21020
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 1.75 1.78 0.775
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.75 24.05 19930 1089 99.9 0.179 0.177 0.208 0.2005 RANDOM 21.76
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] 1.16 -1.62 -0.7 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.61 r_dihedral_angle_4_deg 20.145 r_dihedral_angle_3_deg 15.364 r_dihedral_angle_1_deg 7.792 r_long_range_B_refined 7.066 r_long_range_B_other 6.962 r_scangle_other 4.459 r_mcangle_it 3.301 r_mcangle_other 3.299 r_scbond_it 2.876
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.61 r_dihedral_angle_4_deg 20.145 r_dihedral_angle_3_deg 15.364 r_dihedral_angle_1_deg 7.792 r_long_range_B_refined 7.066 r_long_range_B_other 6.962 r_scangle_other 4.459 r_mcangle_it 3.301 r_mcangle_other 3.299 r_scbond_it 2.876 r_scbond_other 2.874 r_mcbond_it 2.151 r_mcbond_other 2.15 r_angle_refined_deg 1.662 r_angle_other_deg 1.403 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 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 1758 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing