X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
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 85 % saturated citrate, 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.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55 α = 90
b = 55 β = 90
c = 109.21 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 1999-02-17
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 28.92 66.0 0.091 -- -- 2.0 23913 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)
1.47 1.54 33.9 0.25 -- 1.7 -- --

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 1.47 7.5 -- 2.0 -- 21757 2152 66.0 -- 0.192 0.192 0.229 --
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 1.47 1.54 -- 120 1262 0.419 0.462 -- 33.9
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 0.5
x_dihedral_angle_d 26.4
x_angle_deg 3.9
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 37
Solvent Atoms 239

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