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The crystal structure of human Annexin A4 from crystals grown at 4 mM Calcium
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 4.6 295 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 2.38 48.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.613 α = 90 b = 39.62 β = 95.141 c = 73.496 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 EIGER X 16M 2021-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.88560 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.5 73.2 96.8 0.037 11.9 2.7 52824
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 1.5 1.52 0.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 58.377 52808 2649 96.398 0.203 0.2021 0.202 0.2158 0.2165 21.672
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] -0.001 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.098 r_dihedral_angle_3_deg 12.734 r_dihedral_angle_2_deg 7.543 r_lrange_it 6.436 r_lrange_other 6.37 r_dihedral_angle_1_deg 5.848 r_scangle_it 5.418 r_scangle_other 5.345 r_scbond_it 3.651 r_scbond_other 3.553
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.098 r_dihedral_angle_3_deg 12.734 r_dihedral_angle_2_deg 7.543 r_lrange_it 6.436 r_lrange_other 6.37 r_dihedral_angle_1_deg 5.848 r_scangle_it 5.418 r_scangle_other 5.345 r_scbond_it 3.651 r_scbond_other 3.553 r_mcangle_other 2.918 r_mcangle_it 2.908 r_mcbond_it 2.07 r_mcbond_other 2.017 r_angle_refined_deg 1.896 r_angle_other_deg 0.682 r_symmetry_nbd_refined 0.276 r_nbd_refined 0.241 r_nbd_other 0.239 r_nbtor_refined 0.186 r_symmetry_nbd_other 0.178 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.095 r_symmetry_xyhbond_nbd_refined 0.091 r_symmetry_nbtor_other 0.075 r_metal_ion_refined 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 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 171 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing