1C2M

RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.98TRYPSIN-BENZAMIDINE, P3(1) 2 1 WERE GROWN BY VAPOR DIFFUSION, AS DESCRIBED FOR P2(1) 2(1) 2(1) (LARGE CELL) (MANGEL, ET AL., BIOCHEMISTRY 29, 8351-8357, 1990) THE CRYSTAL WAS SOAKED FOR 25 DAYS IN 2.11 M ZN+2, 250 MM CL-, PH 4.86 IN THE ABSENCE OF AN INHIBITOR. THIS SOLUTION WAS REPLACED ONCE EVERY DAY OR TWO TO REMOVE BOUND BENZAMIDINE AND TO INCORPORATE ZN+2 AT THE ACTIVE SITE. IT WAS THEN SOAKED IN CHLORIDE-FREE SOLUTION OF 1.02 MGSO4 . 7H2O, 1.62 M ZNSO4 . 7 H2O, 0.50 M ZINC ACETATE DIHYDRATE, PH 4.98 FOR 10 DAYS DURING WHICH THE SOAKING SOLUTION WAS REPLACED ONCE A DAY.
Crystal Properties
Matthews coefficientSolvent content
2.0318

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.85α = 90
b = 54.85β = 90
c = 109.23γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATERIGAKU RAXIS IV++MSC MIRRORS1998-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

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
11.3335.84740.0858.22.3323740.5
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)
1.41.4637.40.3451.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONDIFFERENCE FOURIER PLUS REFINEMENTX-PLOR1.47.51.7281182864740.1950.1950.234
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]
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d26.2
x_angle_deg3.7
x_improper_angle_d0.52
x_bond_d0.018
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d26.2
x_angle_deg3.7
x_improper_angle_d0.52
x_bond_d0.018
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3297
Nucleic Acid Atoms
Solvent Atoms639
Heterogen Atoms8

Software

Software
Software NamePurpose
bioteXdata collection
bioteXdata reduction
X-PLORmodel building
Quantamodel building
Insight IImodel building
X-PLORrefinement
bioteXdata scaling
X-PLORphasing