5Y9L
Human kallikrein 7 in complex with 1,3,6-trisubstituted 1,4-diazepane-7-one
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2QXI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | PEG1000, PEG3350, 2-methyl-2,4-pentanediol, sodium nitrate, sodium hydrogen phosphate, ammonium sulfate, bicine/trizma buffer |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.895 | α = 90 |
b = 90.926 | β = 90 |
c = 92.03 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 2 |
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 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2010-12-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.54178 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.15 | 100 | 87.8 | 11.4 | 5.2 | 12132 |
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 | 2QXI | 2.15 | 33.68 | 11541 | 583 | 87.87 | 0.21138 | 0.20823 | 0.27555 | RANDOM | 23.168 |
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] | |
-0.16 | -0.3 | 0.46 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.964 |
r_dihedral_angle_4_deg | 23.059 |
r_dihedral_angle_3_deg | 19.118 |
r_dihedral_angle_1_deg | 7.23 |
r_long_range_B_refined | 4.088 |
r_long_range_B_other | 4.075 |
r_scangle_other | 2.617 |
r_mcangle_it | 1.995 |
r_mcangle_other | 1.995 |
r_angle_refined_deg | 1.773 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1706 |
Nucleic Acid Atoms | |
Solvent Atoms | 67 |
Heterogen Atoms | 36 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
AMoRE | phasing |