X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 5.5
Details trypsin-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 in a solution of 1.73 M MgSO4 . 7 H2O, 150 mM MES, 1 mM CaCl2, 2.0 % DMSO,saturated with inhibitor, pH 5.50 over a period of several days with several replacements of the soaking solution., VAPOR DIFFUSION

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.91 α = 90
b = 54.91 β = 90
c = 109.2 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ MSC MIRRORS 1998-03-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE -- -- -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.33 35.86 81.0 0.09 -- -- 3.4 33791 n/a -- 1.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.37 1.43 35.6 0.205 -- 2.2 -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
DIFFERENCE FOURIER PLUS REFINEMENT 1.37 7.5 -- 1.8 -- 33044 3293 81.0 -- 0.181 0.181 0.195 --
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.37 1.43 -- 181 1585 0.4 0.399 -- --
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 0.54
x_dihedral_angle_d 26.2
x_angle_deg 3.8
x_bond_d 0.018
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1629
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 209

Software

Computing
Computing Package Purpose
BIOTEX (MSC) Data Reduction (intensity integration)
BIOTEX Data Reduction (data scaling)
X-PLOR 3.1, QUANTA, INSIGHTII Structure Solution
X-PLOR 3.1 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.1 refinement
INSIGHTII model building
QUANTA model building
X-PLOR version: 3.1 model building
BIOTEX version: (MSC) data reduction
BIOTEX version: (MSC) data collection