4BXS

Crystal Structure of the Prothrombinase Complex from the Venom of Pseudonaja Textilis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KIGUNPUBLISHED FV STRUCTURE AND PDB ENTRY 1KIG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
180.1 M MORPHEUS BUFFER 3, 20% MORPHEUS P20K_P550MME, 50 MM MORPHEUS CARBOXYLIC ACIDS, pH 8
Crystal Properties
Matthews coefficientSolvent content
3.7266.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.31α = 90
b = 115.31β = 90
c = 429.52γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2012-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
13.32101.5999.40.157.8643913
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)
13.323.595.111.55.4

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 REPLACEMENTTHROUGHOUTUNPUBLISHED FV STRUCTURE AND PDB ENTRY 1KIG3.3289.8141486224199.10.301240.297730.36793RANDOM117.583
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]
6.176.17-12.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.056
r_dihedral_angle_3_deg15.819
r_dihedral_angle_4_deg15.057
r_dihedral_angle_1_deg3.872
r_angle_refined_deg0.614
r_chiral_restr0.042
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.056
r_dihedral_angle_3_deg15.819
r_dihedral_angle_4_deg15.057
r_dihedral_angle_1_deg3.872
r_angle_refined_deg0.614
r_chiral_restr0.042
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10995
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms188

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing