2RIV

Crystal structure of the reactive loop cleaved human Thyroxine Binding Globulin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QMBPDB ENTRY 1QMB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7.429820% PEG 3350, 0.2M sodium sulphate, pH 7.4, EVAPORATION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.448.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 173.136α = 90
b = 42.585β = 90
c = 55.989γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4mirrors2007-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.11.5419SRSPX14.1

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
11.529.598.50.04128.96.8640196305922
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)
11.51.53984.80.2227.54.53930

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)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 1QMB1.529.457.526305963059335598.540.190.188750.21401RANDOM18.913
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]
-0.461.2-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.284
r_dihedral_angle_4_deg17.044
r_dihedral_angle_3_deg12.714
r_dihedral_angle_1_deg5.593
r_scangle_it3.03
r_scbond_it1.974
r_angle_refined_deg1.31
r_mcangle_it1.22
r_mcbond_it0.812
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.284
r_dihedral_angle_4_deg17.044
r_dihedral_angle_3_deg12.714
r_dihedral_angle_1_deg5.593
r_scangle_it3.03
r_scbond_it1.974
r_angle_refined_deg1.31
r_mcangle_it1.22
r_mcbond_it0.812
r_nbtor_refined0.305
r_nbd_refined0.205
r_symmetry_vdw_refined0.17
r_symmetry_hbond_refined0.157
r_xyhbond_nbd_refined0.12
r_chiral_restr0.085
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms2935
Nucleic Acid Atoms
Solvent Atoms428
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing