4RKO

Crystal structure of thrombin mutant S195T bound with PPACK


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SHHPDB ID 1SHH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1 M MES, pH 6.5, 15% PEG 6000 and 5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1141.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.593α = 90
b = 73.31β = 113.43
c = 48.706γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2014-06-20MSINGLE 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
11.8440920.08113.43.72476022779-1-1
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)
11.841.8886.80.5181.83.11072

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 ID 1SHH1.8440-1-12360821578115791.40.167960.166090.20224RANDOM40.172
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]
-1.080.21-1.311.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.972
r_dihedral_angle_3_deg13.343
r_dihedral_angle_4_deg13.068
r_dihedral_angle_1_deg7.91
r_long_range_B_refined7.696
r_long_range_B_other7.641
r_scangle_other5.592
r_scbond_it3.649
r_scbond_other3.649
r_mcangle_it3.425
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.972
r_dihedral_angle_3_deg13.343
r_dihedral_angle_4_deg13.068
r_dihedral_angle_1_deg7.91
r_long_range_B_refined7.696
r_long_range_B_other7.641
r_scangle_other5.592
r_scbond_it3.649
r_scbond_other3.649
r_mcangle_it3.425
r_mcangle_other3.424
r_mcbond_it2.428
r_mcbond_other2.428
r_angle_refined_deg1.326
r_angle_other_deg0.836
r_chiral_restr0.15
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2352
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms69

Software

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