9AW9 | pdb_00009aw9

Crystal structure of trypsin at 150 Kelvin with benzamidine (duplicate)


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
2.2745.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.474α = 90
b = 58.286β = 90
c = 66.751γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray150CMOSBRUKER PHOTON 1002023-11-03MSINGLE 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
11.49524.68899.210.71712.231034048
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)
11.524.680.717

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-VALUE1.49524.68834048169297.1220.2040.20290.21230.23440.24459.36
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]
-0.195-0.0110.206
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg15.494
r_dihedral_angle_6_deg13.353
r_dihedral_angle_3_deg11.433
r_dihedral_angle_1_deg7.317
r_lrange_it5.358
r_lrange_other4.53
r_scangle_it2.449
r_scangle_other2.449
r_angle_refined_deg1.768
r_mcangle_it1.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg15.494
r_dihedral_angle_6_deg13.353
r_dihedral_angle_3_deg11.433
r_dihedral_angle_1_deg7.317
r_lrange_it5.358
r_lrange_other4.53
r_scangle_it2.449
r_scangle_other2.449
r_angle_refined_deg1.768
r_mcangle_it1.7
r_mcangle_other1.7
r_scbond_it1.617
r_scbond_other1.616
r_mcbond_it1.14
r_mcbond_other1.137
r_dihedral_angle_other_2_deg0.803
r_angle_other_deg0.615
r_xyhbond_nbd_refined0.289
r_nbd_refined0.215
r_symmetry_nbd_other0.195
r_symmetry_xyhbond_nbd_refined0.193
r_nbtor_refined0.175
r_nbd_other0.158
r_symmetry_nbd_refined0.148
r_metal_ion_refined0.125
r_chiral_restr0.091
r_symmetry_nbtor_other0.085
r_symmetry_xyhbond_nbd_other0.044
r_bond_refined_d0.01
r_gen_planes_refined0.01
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 Atoms326
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SCALAdata scaling
MOLREPphasing