4KTS | pdb_00004kts

Bovine trypsin in complex with microviridin J at pH 8.5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MYWPDB ENTRY 3MYW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.1 M Tris, 0.2 M lithium sulfate, 25% PEG 3350 , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6353.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.33α = 90
b = 64.49β = 90
c = 71.21γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
11.33099.50.04320.65.2656196529122
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)
11.31.499.60.4484.6

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 (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3MYW1.3156529162025326599.540.107160.106060.110.128290.13RANDOM16.505
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]
1.23-0.5-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free40.387
r_dihedral_angle_2_deg39.926
r_dihedral_angle_4_deg12.741
r_dihedral_angle_3_deg10.07
r_sphericity_bonded9.91
r_dihedral_angle_1_deg6.593
r_rigid_bond_restr5.926
r_scbond_it2.526
r_angle_refined_deg2.086
r_mcangle_it1.674
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free40.387
r_dihedral_angle_2_deg39.926
r_dihedral_angle_4_deg12.741
r_dihedral_angle_3_deg10.07
r_sphericity_bonded9.91
r_dihedral_angle_1_deg6.593
r_rigid_bond_restr5.926
r_scbond_it2.526
r_angle_refined_deg2.086
r_mcangle_it1.674
r_mcbond_it1.345
r_mcbond_other1.306
r_angle_other_deg0.996
r_chiral_restr0.149
r_bond_refined_d0.023
r_gen_planes_refined0.011
r_bond_other_d0.007
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1750
Nucleic Acid Atoms
Solvent Atoms349
Heterogen Atoms8

Software

Software
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling