3T29

TMAO-grown trigonal trypsin (bovine)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1C1NPDB entry 1C1N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP1029840 mg/mL protein in 50 mM benzamidine, 3 M TMAO, 0.2 M LiNO3, 0.1 M boric acid, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9336.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.37α = 90
b = 54.37β = 90
c = 105.355γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDOXFORD ONYX CCD2011-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOXFORD DIFFRACTION NOVA1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.7547.199.50.098.93.71874518745
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8497.80.2450.2453.12.7

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 1C1N1.7519.56187451774696099.440.147910.145630.19002RANDOM14.688
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]
-0.61-0.3-0.610.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.725
r_dihedral_angle_4_deg13.802
r_dihedral_angle_3_deg12.668
r_dihedral_angle_1_deg6.577
r_scangle_it3.532
r_scbond_it2.266
r_mcangle_it1.474
r_angle_refined_deg1.456
r_mcbond_it0.827
r_chiral_restr0.105
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.725
r_dihedral_angle_4_deg13.802
r_dihedral_angle_3_deg12.668
r_dihedral_angle_1_deg6.577
r_scangle_it3.532
r_scbond_it2.266
r_mcangle_it1.474
r_angle_refined_deg1.456
r_mcbond_it0.827
r_chiral_restr0.105
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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 Atoms241
Heterogen Atoms45

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrysalisProdata collection
CrysalisProdata reduction