2WYJ
Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with monoaryl P4 motifs
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1EZQ | PDB ENTRY 1EZQ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.75 | CRYSTALLISATION WAS CARRIED OUT USING HANG DROP VAPOUR DIFFUSION METHODS IN 2UL DROPS CONTAINING 1:1 RATIO PROTEIN AND WELL SOLUTION. WELL SOLUTION CONTAINED 16-20% PEG6K, 50MM MES-NAOH (PH5.5-6), 5MM CACL2 AND 50MM NACL, pH 5.75 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.83 | 32.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.564 | α = 90 |
b = 72.485 | β = 90 |
c = 78.177 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC CCD | 2003-11-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | ESRF | ID14-4 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.38 | 30 | 98.2 | 0.06 | 22.7 | 4.3 | 13086 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.38 | 2.49 | 96.4 | 0.37 | 4 | 4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1EZQ | 2.38 | 28.4 | 12423 | 637 | 100 | 0.19979 | 0.19692 | 0.25478 | RANDOM | 51.775 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.86 | -2.39 | 3.25 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 26.678 |
r_dihedral_angle_4_deg | 15.896 |
r_dihedral_angle_3_deg | 11.453 |
r_scangle_it | 5.358 |
r_dihedral_angle_1_deg | 3.671 |
r_scbond_it | 3.469 |
r_mcangle_it | 2.741 |
r_angle_refined_deg | 1.525 |
r_mcbond_it | 1.377 |
r_chiral_restr | 0.108 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2204 |
Nucleic Acid Atoms | |
Solvent Atoms | 91 |
Heterogen Atoms | 30 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | phasing |