3APU

Crystal structure of the A variant of human alpha1-acid glycoprotein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BX6PDB ENTRY 3BX6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.629330% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
238.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.107α = 90
b = 44.862β = 91.88
c = 120.784γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker DIP-60402008-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.15099.90.04456.82125821258
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.1899.30.3266.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3BX62.131.9920189103899.860.20120.19960.23168RANDOM51.507
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]
0.4-0.10.68-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.022
r_dihedral_angle_3_deg17.119
r_dihedral_angle_4_deg14.928
r_dihedral_angle_1_deg6.357
r_scangle_it2.866
r_scbond_it1.78
r_angle_refined_deg1.336
r_mcangle_it1.273
r_mcbond_it0.681
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.022
r_dihedral_angle_3_deg17.119
r_dihedral_angle_4_deg14.928
r_dihedral_angle_1_deg6.357
r_scangle_it2.866
r_scbond_it1.78
r_angle_refined_deg1.336
r_mcangle_it1.273
r_mcbond_it0.681
r_nbtor_refined0.31
r_symmetry_vdw_refined0.234
r_nbd_refined0.209
r_xyhbond_nbd_refined0.156
r_symmetry_hbond_refined0.147
r_chiral_restr0.095
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 AtomsNumber
Protein Atoms2903
Nucleic Acid Atoms
Solvent Atoms83
Heterogen Atoms26

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling