5FFN

Complex of subtilase SubTY from Bacillus sp. TY145 with chymotrypsin inhibitor CI2A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5291Complex was concentrated to 45 mg/ml in 10 mM Tris, pH 7.0. 1 microliter of protein solution with 1 microliter of a reservoir solution containing 5.5 M sodium formate, 0.2 M imidazole-malate pH 6.5, and 200 mM NDSB 201.
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.753α = 90
b = 66.838β = 90
c = 107.082γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMAR scanner 345 mm plate2001-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.8251000.07338.44005440054-317.676
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8399.60.3475.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1SVN1.82538044200999.880.152850.150980.18839RANDOM14.614
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]
0.28-0.810.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.192
r_dihedral_angle_4_deg16.02
r_dihedral_angle_3_deg13.185
r_dihedral_angle_1_deg6.161
r_scangle_it3.61
r_scbond_it2.361
r_angle_refined_deg1.509
r_mcangle_it1.463
r_angle_other_deg0.88
r_mcbond_it0.877
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.192
r_dihedral_angle_4_deg16.02
r_dihedral_angle_3_deg13.185
r_dihedral_angle_1_deg6.161
r_scangle_it3.61
r_scbond_it2.361
r_angle_refined_deg1.509
r_mcangle_it1.463
r_angle_other_deg0.88
r_mcbond_it0.877
r_mcbond_other0.28
r_symmetry_hbond_refined0.251
r_nbd_refined0.211
r_nbd_other0.19
r_xyhbond_nbd_refined0.173
r_nbtor_refined0.172
r_symmetry_vdw_other0.165
r_metal_ion_refined0.099
r_chiral_restr0.095
r_symmetry_vdw_refined0.094
r_nbtor_other0.086
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2753
Nucleic Acid Atoms
Solvent Atoms446
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
XTALVIEWmodel building