4LZ4

X-ray structure of the complex between human thrombin and the TBA deletion mutant lacking thymine 3 nucleobase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729360% Tacsimate, 1-3% MPEG 5K or PEG 8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.2562.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.736α = 90
b = 120.725β = 94.22
c = 67.233γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2MMIRROR2012-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.009ELETTRA5.2R

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
12.555094.40.13229590
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)
12.552.6395.40.397

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT2.5629.6227048143090.260.171140.171140.168270.22675RANDOM37.877
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_deg32.734
r_dihedral_angle_3_deg16.2
r_dihedral_angle_4_deg15.003
r_long_range_B_refined7.64
r_long_range_B_other7.572
r_dihedral_angle_1_deg6.893
r_scangle_other5.876
r_scbond_it3.784
r_scbond_other3.784
r_mcangle_it3.761
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.734
r_dihedral_angle_3_deg16.2
r_dihedral_angle_4_deg15.003
r_long_range_B_refined7.64
r_long_range_B_other7.572
r_dihedral_angle_1_deg6.893
r_scangle_other5.876
r_scbond_it3.784
r_scbond_other3.784
r_mcangle_it3.761
r_mcangle_other3.76
r_mcbond_it2.495
r_mcbond_other2.494
r_angle_refined_deg1.693
r_angle_other_deg1.304
r_chiral_restr0.097
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.004
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4708
Nucleic Acid Atoms612
Solvent Atoms219
Heterogen Atoms92

Software

Software
Software NamePurpose
CCP4refinement
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling