3SQH

Crystal structure of prethrombin-2 mutant S195A in the the open form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HAGpdb entry 1HAG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52950.1 M Tris, 11% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 8.5
Crystal Properties
Matthews coefficientSolvent content
1.9737.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.359α = 90
b = 60.043β = 96.47
c = 49.691γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2011-04-20MSINGLE 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
12.24098.80.0815.74.61336413204-0.8-0.8
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)
12.22.2497.90.323.53.7662

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 1HAG2.230.17-0.8-0.8126141244366198.640.191850.189070.24382RANDOM43.917
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]
0.210.07-0.09-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.101
r_dihedral_angle_3_deg20.833
r_dihedral_angle_4_deg18.681
r_dihedral_angle_1_deg6.995
r_scangle_it2.601
r_scbond_it1.699
r_angle_refined_deg1.444
r_mcangle_it1.078
r_mcbond_it0.588
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.101
r_dihedral_angle_3_deg20.833
r_dihedral_angle_4_deg18.681
r_dihedral_angle_1_deg6.995
r_scangle_it2.601
r_scbond_it1.699
r_angle_refined_deg1.444
r_mcangle_it1.078
r_mcbond_it0.588
r_chiral_restr0.101
r_bond_refined_d0.012
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2304
Nucleic Acid Atoms
Solvent Atoms82
Heterogen Atoms

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling