4BXW

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 1HCGMODEL BASED ON PDB ENTRY 1HCG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.545MM MES PH 5.5 AND 5.6% PVP K12
Crystal Properties
Matthews coefficientSolvent content
3.8367.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 179.31α = 90
b = 179.31β = 90
c = 179.31γ = 90
Symmetry
Space GroupI 21 3

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
12.7173.210.1210.35.526001
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)
12.712.8599.30.692.45.2

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 REPLACEMENTTHROUGHOUTMODEL BASED ON PDB ENTRY 1HCG2.7173.224649135199.840.159170.155370.23308RANDOM41.196
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]
-24.827.74-22.16-29.23-15.254.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.903
r_dihedral_angle_3_deg13.396
r_dihedral_angle_4_deg11.375
r_dihedral_angle_1_deg4.103
r_angle_refined_deg0.669
r_chiral_restr0.047
r_bond_refined_d0.003
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.903
r_dihedral_angle_3_deg13.396
r_dihedral_angle_4_deg11.375
r_dihedral_angle_1_deg4.103
r_angle_refined_deg0.669
r_chiral_restr0.047
r_bond_refined_d0.003
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 Atoms4300
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms69

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing