3GIC

Structure of thrombin mutant delta(146-149e) in the free form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GP9PDB code 2GP9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529320% PEG 20000, 100 mM Tris buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0860.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.229α = 90
b = 58.229β = 90
c = 119.559γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-12-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.90020APS14-BM-C

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
11.5524.1994.30.03727.7284.15424054240
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)
11.551.6176.10.2792.31.94359

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB code 2GP91.5524.195424054226274794.280.1880.1880.1870.22RANDOM15.011
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]
0.580.58-1.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.615
r_dihedral_angle_3_deg15.58
r_dihedral_angle_4_deg12.62
r_dihedral_angle_1_deg6.461
r_scangle_it3.176
r_scbond_it1.947
r_mcangle_it1.463
r_angle_refined_deg1.421
r_mcbond_it0.799
r_chiral_restr0.108
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.615
r_dihedral_angle_3_deg15.58
r_dihedral_angle_4_deg12.62
r_dihedral_angle_1_deg6.461
r_scangle_it3.176
r_scbond_it1.947
r_mcangle_it1.463
r_angle_refined_deg1.421
r_mcbond_it0.799
r_chiral_restr0.108
r_bond_refined_d0.011
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2240
Nucleic Acid Atoms
Solvent Atoms257
Heterogen Atoms14

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction