3JZ2

Crystal structure of human thrombin mutant N143P in E* form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BEIPEB entry 3BEI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82950.1M imidazole and 7% PEG 8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.9658.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.89α = 90
b = 57.89β = 90
c = 119.77γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2009-08-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOTHER1.54

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
12.44096.70.076195.61545214942-1-1
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)
12.42.4477.80.4082.22.8595

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 REPLACEMENTTHROUGHOUTPEB entry 3BEI2.425.3-3-3146291416774796.840.191940.189060.24649RANDOM33.721
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.677
r_dihedral_angle_3_deg16.764
r_dihedral_angle_4_deg16.319
r_dihedral_angle_1_deg6.566
r_scangle_it2.949
r_scbond_it1.782
r_angle_refined_deg1.431
r_mcangle_it1.251
r_mcbond_it0.657
r_chiral_restr0.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.677
r_dihedral_angle_3_deg16.764
r_dihedral_angle_4_deg16.319
r_dihedral_angle_1_deg6.566
r_scangle_it2.949
r_scbond_it1.782
r_angle_refined_deg1.431
r_mcangle_it1.251
r_mcbond_it0.657
r_chiral_restr0.096
r_bond_refined_d0.012
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2234
Nucleic Acid Atoms
Solvent Atoms116
Heterogen Atoms38

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling