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The crystal structure of human Annexin A4 derived from crystals grown in 40 mM of CaCl2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZOC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 0.1 M sodium acetate (pH 4.6), 0.2 M ammonium sulfate, and 25 % (v/v) PEG 4000.
Crystal Properties Matthews coefficient Solvent content 2.34 47.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.742 α = 90 b = 39.906 β = 93.91 c = 73.456 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 X 9M 2022-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.991874 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.27 58.6 95.8 0.059 0.089 0.059 7.8 2.2 86437
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.27 1.29 91.7 0.6
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.27 58.6 86419 4312 95.599 0.175 0.1739 0.1891 0.196 11.972
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] -0.002 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.851 r_dihedral_angle_3_deg 11.381 r_dihedral_angle_2_deg 7.84 r_dihedral_angle_1_deg 6.039 r_lrange_it 5.391 r_lrange_other 5.355 r_scangle_it 4.018 r_scangle_other 3.974 r_scbond_it 2.92 r_scbond_other 2.774
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.851 r_dihedral_angle_3_deg 11.381 r_dihedral_angle_2_deg 7.84 r_dihedral_angle_1_deg 6.039 r_lrange_it 5.391 r_lrange_other 5.355 r_scangle_it 4.018 r_scangle_other 3.974 r_scbond_it 2.92 r_scbond_other 2.774 r_angle_refined_deg 1.896 r_mcangle_other 1.877 r_mcangle_it 1.868 r_mcbond_it 1.285 r_mcbond_other 1.252 r_angle_other_deg 0.666 r_symmetry_nbd_refined 0.313 r_nbd_other 0.301 r_nbd_refined 0.255 r_symmetry_xyhbond_nbd_refined 0.213 r_nbtor_refined 0.185 r_symmetry_nbd_other 0.171 r_xyhbond_nbd_refined 0.124 r_xyhbond_nbd_other 0.1 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.072 r_metal_ion_refined 0.055 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2499 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing