9AWM | pdb_00009awm

Crystal structure of trypsin at 225 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
2.244.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.866α = 90
b = 57.041β = 90
c = 66.72γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray225CMOSBRUKER PHOTON 1002023-11-06MSINGLE 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
11.49923.5993.810.8087.511033354
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)
11.523.580.808

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-VALUE1.49923.5933354165299.0730.1930.19110.19120.21860.218813.447
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]
-0.0360.089-0.053
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg14.692
r_dihedral_angle_6_deg14.397
r_dihedral_angle_3_deg11.589
r_dihedral_angle_1_deg6.717
r_lrange_it5.664
r_lrange_other5.421
r_scangle_it3.671
r_scangle_other3.671
r_scbond_it2.379
r_scbond_other2.377
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg14.692
r_dihedral_angle_6_deg14.397
r_dihedral_angle_3_deg11.589
r_dihedral_angle_1_deg6.717
r_lrange_it5.664
r_lrange_other5.421
r_scangle_it3.671
r_scangle_other3.671
r_scbond_it2.379
r_scbond_other2.377
r_mcangle_it2.371
r_mcangle_other2.37
r_angle_refined_deg1.718
r_mcbond_it1.491
r_mcbond_other1.489
r_dihedral_angle_other_2_deg1.011
r_angle_other_deg0.608
r_xyhbond_nbd_refined0.323
r_symmetry_xyhbond_nbd_refined0.248
r_nbd_refined0.22
r_symmetry_nbd_other0.204
r_nbd_other0.18
r_nbtor_refined0.175
r_symmetry_nbd_refined0.162
r_metal_ion_refined0.127
r_chiral_restr0.089
r_symmetry_nbtor_other0.083
r_symmetry_xyhbond_nbd_other0.032
r_bond_refined_d0.009
r_gen_planes_refined0.009
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 Atoms193
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SCALAdata scaling
MOLREPphasing