X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.72
Details trypsin-benzamidine, P3(1) 2 1 crystals 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 inhibitor-free solution of 1.84 M MgSO4 . 7 H2O, 150 mM Tris, 1 mM CaCl2, pH 7.72 over a period of several weeks with several replacements of the soaking solution.

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 1999-02-09
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 28.9 61.0 0.107 -- -- 1.9 22066 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)
1.48 1.55 33.0 0.269 -- 1.5 -- --

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 1.48 7.5 -- 2.0 -- 19554 1912 61.0 -- 0.198 0.198 0.223 --
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 1.48 1.55 -- 148 1166 0.428 0.468 -- 33.0
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 0.56
x_dihedral_angle_d 26.3
x_angle_deg 3.8
x_bond_d 0.019
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1629
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 289

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