6V5T

Crystal structure of human prethrombin-2 with tryptophans replaced by 5-F-tryptophan


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SQH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.1M Hepes pH 7.5, 25% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.0339.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.545α = 90
b = 58.887β = 98.42
c = 52.455γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2018-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODECu FINE FOCUS1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.14099.30.073182.715696
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)
12.12.140.559

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 REPLACEMENTTHROUGHOUT3SQH2.138.961491177299.20.17990.17720.2297RANDOM38.791
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]
-0.570.170.180.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.237
r_dihedral_angle_3_deg18.073
r_dihedral_angle_4_deg12.675
r_dihedral_angle_1_deg8.258
r_angle_refined_deg1.534
r_angle_other_deg1.25
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.237
r_dihedral_angle_3_deg18.073
r_dihedral_angle_4_deg12.675
r_dihedral_angle_1_deg8.258
r_angle_refined_deg1.534
r_angle_other_deg1.25
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2356
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms11

Software

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