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Crystal structure of Ca-bound human Annexin A5 in low salt condition
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XO3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 287 0.2 M Potassium Citrate Tribasic pH 8.3
0.1 M HEPES pH 7.5
17% PEG3350
50uM CaCl2
2mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.22 44.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.795 α = 90 b = 92.795 β = 90 c = 134.055 γ = 120
Symmetry Space Group P 63 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 193.15 PIXEL DECTRIS PILATUS 6M 2016-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.2325 PAL/PLS 5C (4A)
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 2.747 50 98.8 0.145 0.149 0.032 14.8 16.8 9341
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.8 87.4 0.39 0.415 0.134 0.35 3.5 7.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2XO3 2.747 46.397 1.58 8874 445 94.03 0.253 0.2503 0.2497 0.306 0.3089
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.047 f_angle_d 0.411 f_chiral_restr 0.03 f_bond_d 0.002 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2496 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 3
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing