5EDM

Crystal structure of prothrombin deletion mutant residues 154-167 ( Form I )


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4O03PDB CODE 4O03

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1 M MES, pH 6.5 and 1.6 M MgSO4
Crystal Properties
Matthews coefficientSolvent content
5.1673.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.884α = 90
b = 168.69β = 90
c = 144.315γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2014-08-14MSINGLE 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
12.292.07980.087177.367055-0.3
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)
12.22.2497.80.48734.4

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 REPLACEMENTTHROUGHOUTPDB CODE 4O032.292.07633623409980.1980.1960.236RANDOM59.17
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]
-0.78-1.21.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.131
r_dihedral_angle_4_deg16.922
r_dihedral_angle_3_deg16.169
r_long_range_B_refined9.711
r_long_range_B_other9.627
r_dihedral_angle_1_deg6.623
r_scangle_other4.728
r_scbond_it3.603
r_scbond_other3.497
r_mcangle_it2.824
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.131
r_dihedral_angle_4_deg16.922
r_dihedral_angle_3_deg16.169
r_long_range_B_refined9.711
r_long_range_B_other9.627
r_dihedral_angle_1_deg6.623
r_scangle_other4.728
r_scbond_it3.603
r_scbond_other3.497
r_mcangle_it2.824
r_mcangle_other2.824
r_mcbond_it1.706
r_mcbond_other1.706
r_angle_refined_deg1.681
r_angle_other_deg0.812
r_chiral_restr0.116
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms4414
Nucleic Acid Atoms
Solvent Atoms464
Heterogen Atoms138

Software

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