3RXT

Crystal structure of Trypsin complexed with (3-methoxyphenyl)methanamin (F04 and F03, cocktail experiment)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S0RPDB ENTRY 1S0R

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52770.1M Tris-HCl, 30% PEG 3350, 0.2M Lithium Sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2645.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.537α = 90
b = 57.911β = 90
c = 66.625γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.75098.70.060.06623633-316.8

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1S0R1.719.852235722221117199.390.176980.175730.20083RANDOM11.604
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]
-0.250.5-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.855
r_dihedral_angle_4_deg19.089
r_dihedral_angle_3_deg10.937
r_dihedral_angle_1_deg6.078
r_scangle_it1.814
r_scbond_it1.206
r_angle_refined_deg1.076
r_angle_other_deg0.788
r_mcangle_it0.745
r_mcbond_it0.503
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.855
r_dihedral_angle_4_deg19.089
r_dihedral_angle_3_deg10.937
r_dihedral_angle_1_deg6.078
r_scangle_it1.814
r_scbond_it1.206
r_angle_refined_deg1.076
r_angle_other_deg0.788
r_mcangle_it0.745
r_mcbond_it0.503
r_symmetry_vdw_refined0.297
r_nbd_refined0.234
r_symmetry_vdw_other0.227
r_symmetry_hbond_refined0.214
r_nbd_other0.187
r_nbtor_refined0.171
r_xyhbond_nbd_refined0.09
r_nbtor_other0.084
r_mcbond_other0.084
r_chiral_restr0.064
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1629
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms27

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling