3ELA

Crystal structure of active site inhibited coagulation factor VIIA mutant 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 DROP5.6298100mM NaCitrate, 16%(w/v) PEG4000, 12%(v/v) 1-propanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.0659.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.361α = 90
b = 68.558β = 90.22
c = 78.817γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-31.08MAX III911-3

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
12.229.1980.30.0961.8346583465823.5
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)
12.22.326.10.2292.121.31526

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1DAN2.229.19347193293617341000.235680.232590.2943RANDOM33.911
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]
-2.130.61-2.324.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.327
r_dihedral_angle_4_deg19.654
r_dihedral_angle_3_deg18.403
r_dihedral_angle_1_deg11.67
r_scangle_it3.171
r_angle_refined_deg2.17
r_scbond_it2.124
r_mcangle_it1.667
r_mcbond_it0.958
r_symmetry_vdw_refined0.526
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.327
r_dihedral_angle_4_deg19.654
r_dihedral_angle_3_deg18.403
r_dihedral_angle_1_deg11.67
r_scangle_it3.171
r_angle_refined_deg2.17
r_scbond_it2.124
r_mcangle_it1.667
r_mcbond_it0.958
r_symmetry_vdw_refined0.526
r_nbtor_refined0.319
r_symmetry_hbond_refined0.308
r_nbd_refined0.275
r_xyhbond_nbd_refined0.219
r_metal_ion_refined0.16
r_chiral_restr0.134
r_bond_refined_d0.018
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4119
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms56

Software

Software
Software NamePurpose
MAR345data collection
CCP4model building
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling
CCP4phasing