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139555
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
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Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
1D3T
CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZO[B]THIOPHENE INHIBITOR 1
Display Files
FASTA Sequence
PDB File
PDB File (Header)
mmCIF File
mmCIF File (Header)
PDBML/XML File
PDBML/XML File (Header)
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FASTA Sequence
PDB File (Text)
PDB File (gz)
PDBx/mmCIF File
PDBx/mmCIF File (gz)
PDBML/XML File
PDBML/XML File (gz)
Biological Assembly (gz) (A+S)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Sitting Drop
pH
5.6
Temperature
277.0
Details
30% PEG 3400; 100 mM sodium citrate; 200 mM ammonium acetate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 71.14
α = 90
b = 71.85
β = 100.5
c = 72.96
γ = 90
Symmetry
Space Group
C 1 2 1
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
295
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
IMAGE PLATE
RIGAKU RAXIS IIC
YALE/MSC MIRRORS
1996-01-01
Diffraction Radiation
Monochromator
Protocol
--
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
ROTATING ANODE
RIGAKU RU200
--
--
--
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
3
30
79.7
0.084
--
--
2.1
--
5736
--
0.0
--
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)
3.0
3.05
81.0
0.257
--
3.1
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
--
3.0
20.0
--
2.0
--
5642
436
78.6
--
0.172
0.172
0.235
RANDOM
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
3.0
3.14
--
--
567
0.297
0.398
--
76.5
RMS Deviations
Key
Refinement Restraint Deviation
x_dihedral_angle_d
27.03
x_improper_angle_d
0.96
x_bond_d
0.009
x_angle_deg
1.46
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
2364
Nucleic Acid Atoms
0
Heterogen Atoms
55
Solvent Atoms
0
Software
Software
Software Name
Purpose
DENZO
data reduction
SCALEPACK
data scaling
X-PLOR
model building
X-PLOR
refinement version: 98.0
X-PLOR
phasing