6QLW
Cathepsin-K in complex with MIV-710
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.1 | 291 | 25mM ADA pH6.1, 250mM sodium nitrate and 20% PEG 5k.mme |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 75.727 | α = 90 |
b = 69.484 | β = 100.89 |
c = 78.68 | 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 | 2008-06-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 1.0723 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 74.473 | 96 | 0.148 | 0.175 | 0.091 | 0.98 | 7 | 3.3 | 52114 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2 | 2.05 | 75.4 | 0.596 | 0.767 | 0.475 | 0.554 | 2.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2 | 74.473 | 49585 | 2517 | 95.82 | 0.182 | 0.1798 | 0.2252 | RANDOM | 21.152 |
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] | |
2.74 | 1.43 | -1.22 | -1.93 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.646 |
r_dihedral_angle_3_deg | 15.379 |
r_dihedral_angle_4_deg | 14.637 |
r_dihedral_angle_1_deg | 5.479 |
r_angle_refined_deg | 1.71 |
r_angle_other_deg | 1.083 |
r_chiral_restr | 0.086 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.008 |
r_gen_planes_other | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6626 |
Nucleic Acid Atoms | |
Solvent Atoms | 899 |
Heterogen Atoms | 165 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |