2PUQ

Crystal structure of active site inhibited coagulation factor VIIA in complex with soluble tissue factor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DANPDB ENTRY 1DAN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62980.1 M sodium citrate, pH 5.6, 16.0 % (w/v) PEG 4000, 12 % (v/v) 1-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.4163.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.312α = 90
b = 68.827β = 90.74
c = 78.732γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2005-06-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.05SLSX06SA

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
12.0539.1599.60.13284.25251152511
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)
12.052.198.90.692.264.13582

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1DAN2.0539.15525105251026261000.2310.2310.2280.273RANDOM39.466
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]
-3.140.69-1.454.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.609
r_dihedral_angle_3_deg17.341
r_dihedral_angle_4_deg16.084
r_dihedral_angle_1_deg15.64
r_mcangle_it3.894
r_scangle_it3.719
r_mcbond_it2.759
r_scbond_it2.72
r_angle_refined_deg2.495
r_nbtor_refined0.338
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.609
r_dihedral_angle_3_deg17.341
r_dihedral_angle_4_deg16.084
r_dihedral_angle_1_deg15.64
r_mcangle_it3.894
r_scangle_it3.719
r_mcbond_it2.759
r_scbond_it2.72
r_angle_refined_deg2.495
r_nbtor_refined0.338
r_nbd_refined0.289
r_symmetry_vdw_refined0.263
r_xyhbond_nbd_refined0.262
r_symmetry_hbond_refined0.208
r_chiral_restr0.194
r_metal_ion_refined0.055
r_bond_refined_d0.028
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4097
Nucleic Acid Atoms
Solvent Atoms187
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction
PHASERphasing