X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Details Thrombin was purchased from Haematologic Technologies, Inc. and acetyl-hirudin from Bachem. Thrombin was prepared as described (Skrzpczak-Jankun et al., 1991). Thrombin (1.0 mg/ml in 50 mM HEPES, 50 % glycerol, pH 7.0) was incubated with 1.0 mM acetyl-hirudin, 10 mM 4-iodobenzo[b]thiophene-2-carboxamidine for 1 hr at 4 deg C. Glycerol was removed andthe complex concentrated with a centricon 10 (Amicon) to about 10 mg/ml as determined by the Biorad protein assay kit using bovine serum albumin. Crystals of thrombin-acetyl-hirudin-4-iodobenzo[b]thiophene-2-carboxamidine were grown in hanging drops by vapor diffusion after streak seeding. The drops were made from 5 microliters of complex and 5 microliters of reservoir solution (0.10 M Tris,0.50 M NaCl, 22 % (by volume) PEG 4K, pH 7.5)., VAPOR DIFFUSION

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.14 α = 90
b = 72.26 β = 101.23
c = 73.09 γ = 90
Symmetry
Space Group C 1 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 1999-04-08
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
1.5 36.13 65.0 0.063 -- -- 2.1 43801 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)
1.5 1.57 36.1 0.245 -- 1.9 -- --

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 1.5 7.5 -- 2.0 -- 37810 3800 65.0 -- 0.22 0.22 0.246 --
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 1.5 1.57 -- 282 2331 0.498 0.508 -- 36.1
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 0.49
x_dihedral_angle_d 26.1
x_angle_deg 4.0
x_bond_d 0.018
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2421
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 255

Software

Computing
Computing Package Purpose
BIOTEX (MSC) Data Reduction (intensity integration)
BIOTEX Data Reduction (data scaling)
X-PLOR, 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 model building
BIOTEX version: (MSC) data reduction
BIOTEX version: (MSC) data collection