4H3X
Crystal structure of an MMP broad spectrum hydroxamate based inhibitor CC27 in complex with the MMP-9 catalytic domain
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4H2E |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | protein: hMMP-9-WT 5.5 mg/mL 120 milli-M acetohydroxamic acid. Reservoir: 10% PEG 20,000, 60mM MES pH 5.5 + 18% MPEG 5,000, 0.08 M imidazole piperidine; pH 8.5, 0.05 M NaCl. Cryoprotectant: 10% Di-ethylene glycol, 10% 1.2-propanediol, 10% glycerol, 10% PEG 10K, 10% PCTP 50/50, 200mM NaCl , VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.34 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.11 | α = 90 |
b = 97.94 | β = 111.73 |
c = 46.08 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 QUANTUM 315r | bent cylindrical mirror | 2011-01-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.8726 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | 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 | 1.76 | 50 | 98 | 0.136 | 0.119 | 8.41 | 4.23 | 32612 | 31957 | -3 | 24.441 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.76 | 1.87 | 94.2 | 0.666 | 0.582 | 2.33 | 4.13 | 5246 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | 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 | 4H2E | 1.764 | 42.806 | -3 | 2 | 31957 | 31949 | 1598 | 98.28 | 0.1993 | 0.1964 | 0.2541 | RANDOM |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 18.451 |
f_angle_d | 1.03 |
f_chiral_restr | 0.074 |
f_bond_d | 0.007 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2608 |
Nucleic Acid Atoms | |
Solvent Atoms | 380 |
Heterogen Atoms | 121 |
Software
Software | |
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Software Name | Purpose |
DNA | data collection |
MOLREP | phasing |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |