☰ Navigation Tabs
Crystal structure of human recombinant Beta-2 glycoprotein I short tag (ST-B2GPI)
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 7.5 277 100 mM HEPES, 1.5 M AmSO4, 20 mM CaCl2 and 2% glycerol
Crystal Properties Matthews coefficient Solvent content 10.87 88.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.248 α = 90 b = 171.16 β = 90 c = 113.369 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 IMAGE PLATE RIGAKU RAXIS IV++ 2015-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE Cu FINE FOCUS 1.5418
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 2.99 116.98 98.8 0.095 13.7 5 31543
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 3 3.05 97.7 0.461 2.4 3.7
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 2.99 116.98 29924 1611 98.5 0.224 0.223 0.2324 0.246 0.2525 RANDOM 75.41
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] 0.92 3.08 -4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.179 r_dihedral_angle_3_deg 19.049 r_dihedral_angle_4_deg 16.058 r_dihedral_angle_1_deg 7.596 r_angle_refined_deg 1.758 r_angle_other_deg 0.985 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.179 r_dihedral_angle_3_deg 19.049 r_dihedral_angle_4_deg 16.058 r_dihedral_angle_1_deg 7.596 r_angle_refined_deg 1.758 r_angle_other_deg 0.985 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2517 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 236
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing