9AWD | pdb_00009awd

Crystal structure of trypsin at 175 Kelvin with benzamidine (triplicate)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.42980.2 M Potassium phosphate dibasic, 20% w/v Polyethylene glycol 3,350.
Crystal Properties
Matthews coefficientSolvent content
2.2545.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.325α = 90
b = 58.226β = 90
c = 66.254γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray175CMOSBRUKER PHOTON 1002023-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER TURBO X-RAY SOURCE1.54184

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.4923.08594.170.65210.911033103
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.523.070.6521

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.49123.08533103162894.6880.2370.2350.2420.26730.27269.37
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]
-0.1270.0230.104
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg17.009
r_dihedral_angle_6_deg13.1
r_dihedral_angle_3_deg10.978
r_dihedral_angle_1_deg7.262
r_lrange_it4.955
r_lrange_other4.081
r_scangle_it2.44
r_scangle_other2.44
r_mcangle_it1.761
r_mcangle_other1.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg17.009
r_dihedral_angle_6_deg13.1
r_dihedral_angle_3_deg10.978
r_dihedral_angle_1_deg7.262
r_lrange_it4.955
r_lrange_other4.081
r_scangle_it2.44
r_scangle_other2.44
r_mcangle_it1.761
r_mcangle_other1.76
r_angle_refined_deg1.715
r_scbond_it1.583
r_scbond_other1.582
r_mcbond_it1.105
r_mcbond_other1.104
r_dihedral_angle_other_2_deg1.089
r_angle_other_deg0.584
r_xyhbond_nbd_refined0.282
r_nbd_refined0.21
r_symmetry_nbd_other0.203
r_nbd_other0.201
r_symmetry_xyhbond_nbd_refined0.2
r_symmetry_nbd_refined0.195
r_nbtor_refined0.176
r_metal_ion_refined0.152
r_symmetry_nbtor_other0.086
r_chiral_restr0.079
r_symmetry_xyhbond_nbd_other0.017
r_gen_planes_refined0.01
r_bond_refined_d0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1629
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SCALAdata scaling
MOLREPphasing