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Crystal structure of V39A mutant of human CEACAM1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QXW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.005 M Cobalt(II) chloride hexahydrate, 0.005 M Nickel(II) chloride hexahydrate, 0.005 M Cadmium chloride hydrate, 0.005 M Magnesium chloride hexahydrate with 12% w/v Polyethylene glycol 3,350 in 0.1 M HEPES pH 7.5 buffer
Crystal Properties Matthews coefficient Solvent content 3.27 62.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.44 α = 90 b = 91.44 β = 90 c = 64.41 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300-HS 2017-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
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 1.9 39.59 100 0.2 0.214 0.076 0.992 7.8 7.7 47459
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 1.9 1.94 100 1.675 1.794 0.642 0.304 7.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4QXW 1.9 39.59 45092 2358 99.96 0.1469 0.1449 0.1347 0.1861 0.1703 RANDOM 27.761
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] 3.75 3.75 -7.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.805 r_dihedral_angle_4_deg 19.577 r_dihedral_angle_3_deg 16.123 r_dihedral_angle_1_deg 8.325 r_angle_refined_deg 2.279 r_angle_other_deg 1.242 r_chiral_restr 0.141 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.805 r_dihedral_angle_4_deg 19.577 r_dihedral_angle_3_deg 16.123 r_dihedral_angle_1_deg 8.325 r_angle_refined_deg 2.279 r_angle_other_deg 1.242 r_chiral_restr 0.141 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3356 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing