4H6S

Crystal structure of thrombin mutant E14eA/D14lA/E18A/S195A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.32950.2M NH4Cl and 20% PEG 3350, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.9135.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.904α = 90
b = 70.828β = 90
c = 56.103γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2011-08-31MSINGLE 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)R Sym 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
12.194097.20.1070.10710.53.71351113133-1-1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.24970.4440.4442.53.3643

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1SHH2.1929.13128911236964695.950.199110.196070.2591RANDOM41.076
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]
0.18-0.16-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.644
r_dihedral_angle_3_deg18.48
r_dihedral_angle_4_deg17.616
r_dihedral_angle_1_deg6.949
r_scangle_it3.311
r_scbond_it1.978
r_angle_refined_deg1.486
r_mcangle_it1.432
r_mcbond_it0.759
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.644
r_dihedral_angle_3_deg18.48
r_dihedral_angle_4_deg17.616
r_dihedral_angle_1_deg6.949
r_scangle_it3.311
r_scbond_it1.978
r_angle_refined_deg1.486
r_mcangle_it1.432
r_mcbond_it0.759
r_chiral_restr0.107
r_bond_refined_d0.012
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2275
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms1

Software

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