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Crystal structure of a calcium- and sodium-bound mouse Olfactomedin-1 disulfide-linked dimer of the Olfactomedin domain and part of coiled coil
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AMO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.08 M Mg Acetate, 30% PEG4000, 0.05 M Na Cacodylate pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.79 55.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.705 α = 90 b = 46.971 β = 117.435 c = 104.952 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 2018-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.89 75.994 92.2 0.06 0.072 0.039 0.998 10.3 3.3 29117 34.574240918
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 1.891 2.101 77.2 0.751 0.893 0.479 0.551 1.7 3.4
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 5AMO 2 71.3 1.34348608369 27170 1459 60.2576245501 0.180557826647 0.178664702636 0.1802 0.215627701203 0.218 49.0864676127
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 12.6603569489 f_angle_d 0.852317911462 f_chiral_restr 0.0638063696724 f_bond_d 0.00654472407717 f_plane_restr 0.00414724978879
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4321 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 133
Software Software Software Name Purpose XDS data reduction PHENIX refinement Aimless data scaling PHASER phasing Coot model building