5EDK

Crystal structure of prothrombin deletion mutant residues 146-167 ( Form II ).


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4O03pdb code 4O03

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.12930.2 M di-Na hydrogen phosphate and 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
4.871.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.192α = 90
b = 84.192β = 90
c = 346.427γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2014-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
13.286.6194.50.15574.42005320053-0.9-0.9
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)
13.23.26940.44123

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 code 4O033.21486.61-0.918675100992.20.292740.291120.32266RANDOM86.358
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]
0.10.1-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.505
r_dihedral_angle_3_deg19.137
r_dihedral_angle_4_deg16.039
r_dihedral_angle_1_deg8.285
r_long_range_B_refined8.194
r_long_range_B_other8.193
r_mcangle_it5.305
r_mcangle_other5.304
r_scangle_other4.248
r_mcbond_it3.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.505
r_dihedral_angle_3_deg19.137
r_dihedral_angle_4_deg16.039
r_dihedral_angle_1_deg8.285
r_long_range_B_refined8.194
r_long_range_B_other8.193
r_mcangle_it5.305
r_mcangle_other5.304
r_scangle_other4.248
r_mcbond_it3.078
r_mcbond_other3.078
r_scbond_it2.359
r_scbond_other2.359
r_angle_refined_deg1.211
r_angle_other_deg0.784
r_chiral_restr0.069
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4242
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing