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Crystal structure of human recombinant Beta-2 glycoprotein I (hrB2GPI)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C1Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 100 mM MES and 1.6 M AMSO4
Crystal Properties Matthews coefficient Solvent content 10.95 88.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.327 α = 90 b = 173.248 β = 90 c = 115.171 γ = 90
Symmetry Space Group C 2 2 21
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 2018-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
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 2.58 49.16 97.1 0.143 10 7.5 48503
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 2.6 2.64 77.1 0.647 1.5 3.4
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 1C1Z 2.58 49.16 45862 2599 95.7 0.202 0.2 0.2143 0.232 0.2377 RANDOM 68.76
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] 1.8 0.66 -2.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.356 r_dihedral_angle_3_deg 18.999 r_dihedral_angle_4_deg 17.184 r_dihedral_angle_1_deg 8.022 r_angle_refined_deg 2.041 r_angle_other_deg 1.244 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.356 r_dihedral_angle_3_deg 18.999 r_dihedral_angle_4_deg 17.184 r_dihedral_angle_1_deg 8.022 r_angle_refined_deg 2.041 r_angle_other_deg 1.244 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2510 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 349
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing