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Crystal structure of the A variant of human alpha1-acid glycoprotein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BX6 PDB ENTRY 3BX6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 30% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 38.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.107 α = 90 b = 44.862 β = 91.88 c = 120.784 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 CCD Bruker DIP-6040 2008-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 2.1 50 99.9 0.044 56.8 21258 21258
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) 2.1 2.18 99.3 0.326 6.7
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 PDB ENTRY 3BX6 2.1 31.99 20189 1038 99.86 0.2012 0.1996 0.2396 0.23168 0.2681 RANDOM 51.507
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] 0.4 -0.1 0.68 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.022 r_dihedral_angle_3_deg 17.119 r_dihedral_angle_4_deg 14.928 r_dihedral_angle_1_deg 6.357 r_scangle_it 2.866 r_scbond_it 1.78 r_angle_refined_deg 1.336 r_mcangle_it 1.273 r_mcbond_it 0.681 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.022 r_dihedral_angle_3_deg 17.119 r_dihedral_angle_4_deg 14.928 r_dihedral_angle_1_deg 6.357 r_scangle_it 2.866 r_scbond_it 1.78 r_angle_refined_deg 1.336 r_mcangle_it 1.273 r_mcbond_it 0.681 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.147 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2903 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 26
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling