2AYW | pdb_00002ayw

Crystal Structure of the complex formed between trypsin and a designed synthetic highly potent inhibitor in the presence of benzamidine at 0.97 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JRT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62905mM MES, 1mM CaCl2, 2.5mM benzamidine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.139

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.55α = 90
b = 68.55β = 90
c = 73.33γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMirror2000-08-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7B0.91EMBL/DESY, HAMBURGBW7B

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
10.972099.60.06518.22252511166647.66
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)
10.97195.50.4013.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1JRT0.9720116664114997116799.60.137730.137730.133550.14260.156830.1635RANDOM9.672
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]
-0.15-0.08-0.150.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.973
r_dihedral_angle_4_deg18.526
r_dihedral_angle_3_deg13.236
r_dihedral_angle_1_deg6.727
r_sphericity_free5.517
r_scangle_it3.27
r_scbond_it3.038
r_angle_other_deg2.908
r_sphericity_bonded2.546
r_rigid_bond_restr1.945
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.973
r_dihedral_angle_4_deg18.526
r_dihedral_angle_3_deg13.236
r_dihedral_angle_1_deg6.727
r_sphericity_free5.517
r_scangle_it3.27
r_scbond_it3.038
r_angle_other_deg2.908
r_sphericity_bonded2.546
r_rigid_bond_restr1.945
r_mcangle_it1.794
r_angle_refined_deg1.66
r_mcbond_it1.284
r_mcbond_other0.548
r_symmetry_vdw_other0.281
r_symmetry_vdw_refined0.244
r_symmetry_hbond_refined0.243
r_nbd_refined0.206
r_nbd_other0.191
r_nbtor_refined0.182
r_xyhbond_nbd_refined0.182
r_chiral_restr0.104
r_metal_ion_refined0.097
r_nbtor_other0.094
r_gen_planes_refined0.019
r_bond_refined_d0.012
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1629
Nucleic Acid Atoms
Solvent Atoms449
Heterogen Atoms105

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
AMoREphasing