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139717
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
1C5S
STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR
Display Files
FASTA Sequence
PDB File
PDB File (Header)
mmCIF File
mmCIF File (Header)
PDBML/XML File
PDBML/XML File (Header)
Download Files
FASTA Sequence
PDB File (Text)
PDB File (gz)
PDBx/mmCIF File
PDBx/mmCIF File (gz)
PDBML/XML File
PDBML/XML File (gz)
Structure Factor (Text)
Structure Factor (gz)
Biological Assembly (gz) (A)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion
pH
8.2
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 MgSO4 . 7 H2O, 100 mM Tris, 1 mM CaCl2, 2.0 % DMSO,saturated with inhibitor, pH 8.20 over a period of several days with several replacements of the soaking solution., VAPOR DIFFUSION
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 55.03
α = 90
b = 55.03
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
1997-12-18
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
35.91
88.0
0.0502
--
--
3.2
37545
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)
1.36
1.42
50.4
0.224
--
2.5
--
--
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
1.36
7.5
--
1.8
--
36792
3693
88.0
--
0.197
0.197
0.224
--
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
1.36
1.42
--
254
2320
0.417
0.448
--
50.4
RMS Deviations
Key
Refinement Restraint Deviation
x_improper_angle_d
0.58
x_bond_d
0.019
x_angle_deg
3.7
x_dihedral_angle_d
26.3
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
3270
Nucleic Acid Atoms
0
Heterogen Atoms
52
Solvent Atoms
612
Software
Software
Software Name
Purpose
bioteX
data collection version: (MSC)
bioteX
data reduction version: (MSC)
X-PLOR
model building version: 3.1
Quanta
model building
Insight II
model building
X-PLOR
refinement version: 3.1
bioteX
data scaling
X-PLOR
phasing version: 3.1