2PW8

Crystal structure of sulfo-hirudin complexed to thrombin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HTC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52980.1M Tris, 20% PEG2K, 0.01M Nickel Chloride. , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4449.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.074α = 90
b = 103.567β = 90
c = 139.184γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42007-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.11.00ALS5.0.1

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
11.8447.9595.750.0992824.634309328515
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.841.9194.60.64510.53.53165

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT4HTC1.8447.9523430932851164995.750.1770.1750.233RANDOM34.397
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]
0.03-0.430.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.292
r_dihedral_angle_4_deg17.902
r_dihedral_angle_3_deg17.347
r_dihedral_angle_1_deg6.194
r_scangle_it5.146
r_scbond_it3.857
r_mcangle_it2.443
r_angle_refined_deg1.643
r_mcbond_it1.615
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.292
r_dihedral_angle_4_deg17.902
r_dihedral_angle_3_deg17.347
r_dihedral_angle_1_deg6.194
r_scangle_it5.146
r_scbond_it3.857
r_mcangle_it2.443
r_angle_refined_deg1.643
r_mcbond_it1.615
r_nbtor_refined0.316
r_xyhbond_nbd_refined0.237
r_nbd_refined0.219
r_symmetry_vdw_refined0.187
r_chiral_restr0.151
r_symmetry_hbond_refined0.133
r_metal_ion_refined0.023
r_bond_refined_d0.016
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2779
Nucleic Acid Atoms
Solvent Atoms221
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing