1V6D

The crystal structure of the trypsin complex with synthetic heterochiral peptide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.42932M ammonium sulphate, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.8733.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.93α = 90
b = 53.719β = 90
c = 77.473γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMARRESEARCH2003-08-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.944.2894.20.0691512915129
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.91.9794.215129

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 REPLACEMENTTHROUGHOUT1QQU1.944.28143611436174094.280.154530.154530.153240.17849RANDOM17.1
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]
-0.770.330.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.04
r_scangle_it6.527
r_scbond_it4.44
r_dihedral_angle_1_deg4.271
r_angle_refined_deg3.554
r_mcangle_it2.545
r_angle_other_deg1.956
r_mcbond_it1.397
r_symmetry_vdw_refined0.841
r_symmetry_vdw_other0.536
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.04
r_scangle_it6.527
r_scbond_it4.44
r_dihedral_angle_1_deg4.271
r_angle_refined_deg3.554
r_mcangle_it2.545
r_angle_other_deg1.956
r_mcbond_it1.397
r_symmetry_vdw_refined0.841
r_symmetry_vdw_other0.536
r_symmetry_hbond_refined0.427
r_nbd_refined0.42
r_xyhbond_nbd_refined0.254
r_nbd_other0.252
r_nbtor_other0.202
r_chiral_restr0.142
r_symmetry_hbond_other0.068
r_xyhbond_nbd_other0.065
r_bond_refined_d0.024
r_gen_planes_refined0.01
r_gen_planes_other0.006
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1690
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing