4MLF

Crystal structure for the complex of thrombin mutant D102N and hirudin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.329320% PEG 3350, 0.2M Ca acetate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.2962.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.506α = 90
b = 89.506β = 90
c = 133.148γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2013-08-11MSINGLE 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
12.274.2895.50.070.0723.811.52826526993-0.5-0.539.5
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)
12.22.2497.60.4810.4813.37.11352

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 entry 1SHH2.240-0.5-0.52678125485134895.160.199960.198180.2335RANDOM52.611
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]
-0.47-0.470.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.182
r_dihedral_angle_3_deg18.531
r_dihedral_angle_4_deg18.206
r_dihedral_angle_1_deg6.798
r_scangle_it2.877
r_scbond_it1.771
r_angle_refined_deg1.463
r_mcangle_it0.923
r_mcbond_it0.487
r_chiral_restr0.105
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.182
r_dihedral_angle_3_deg18.531
r_dihedral_angle_4_deg18.206
r_dihedral_angle_1_deg6.798
r_scangle_it2.877
r_scbond_it1.771
r_angle_refined_deg1.463
r_mcangle_it0.923
r_mcbond_it0.487
r_chiral_restr0.105
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2802
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms27

Software

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