4H6T

Crystal structure of prethrombin-2 mutant E14eA/D14lA/E18A/S195A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.72950.2M KH2PO4 and 20% PEG 3350, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.7855.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.465α = 90
b = 135.465β = 90
c = 42.468γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2011-10-02MSINGLE 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
12.495.7998.80.070.0721.38.71619816004-0.2-0.2
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)
12.42.4497.80.440.442.95750

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 3SQH2.495.79160511507680298.920.213850.211840.25307RANDOM47.882
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]
-0.09-0.090.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.023
r_dihedral_angle_3_deg19.718
r_dihedral_angle_4_deg15.761
r_dihedral_angle_1_deg7.243
r_scangle_it3.438
r_scbond_it2.021
r_mcangle_it1.81
r_angle_refined_deg1.525
r_mcbond_it0.973
r_chiral_restr0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.023
r_dihedral_angle_3_deg19.718
r_dihedral_angle_4_deg15.761
r_dihedral_angle_1_deg7.243
r_scangle_it3.438
r_scbond_it2.021
r_mcangle_it1.81
r_angle_refined_deg1.525
r_mcbond_it0.973
r_chiral_restr0.11
r_bond_refined_d0.014
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2366
Nucleic Acid Atoms
Solvent Atoms63
Heterogen Atoms35

Software

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