X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.98
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 TRANSFERRED TO 0.25 M MES, 1.53 M MGSO4 . 7 H2O, PH 4.98 AND SOAKED FOR MANY DAYS DURING WHICH THE SOAKING SOLUTION WAS REPLACED TO REMOVE BOUND BENZAMIDINE.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.91 α = 90
b = 54.91 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 1998-04-15
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 36.4 71.0 0.105 -- -- 2.7 -- 28493 -- 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)
1.4 1.46 35.9 0.34 -- 1.6 -- --

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 1.4 7.5 -- 2.0 -- 27078 2727 71.0 -- 0.199 0.199 0.231 --
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 1.4 1.46 -- 168 1507 0.418 0.447 -- 35.9
RMS Deviations
Key Refinement Restraint Deviation
x_angle_deg 3.8
x_bond_d 0.019
x_improper_angle_d 0.58
x_dihedral_angle_d 26.5
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3316
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 690

Software

Software
Software Name Purpose
bioteX data collection version: (MSC)
bioteX data reduction version: (MSC)
X-PLOR model building
Quanta model building
Insight II model building
X-PLOR refinement version: 3.1
bioteX data scaling
X-PLOR phasing