2UZJ
Crystal structure of the mature streptococcal cysteine protease, mSpeB
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1DKI | PDB ENTRY 1DKI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 0.2 M (NH4)2SO4, 0.1 M NA-ACETATE, PH 4.0, 20 % PEG4000. PROTEIN KONCENTRATION WAS 0.07 MM (IN 20 MM NA-ACETATE, PH 5.0). |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.52 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 58.828 | ¦Á = 90 |
b = 60.888 | ¦Â = 101.14 |
c = 70.365 | ¦Ã = 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 | IMAGE PLATE | RIGAKU IMAGE PLATE | MIRRORS. MSC-CONFOCAL MAXFLUX | 2008-06-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R |
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 | 1.55 | 21.48 | 90.1 | 0.09 | 15.32 | 4.7 | 63795 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.55 | 1.59 | 55.9 | 0.77 | 0.97 | 2 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1DKI | 1.55 | 21.48 | 60554 | 3238 | 90 | 0.183 | 0.181 | 0.1758 | 0.227 | 0.2222 | RANDOM | 13.33 |
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] | |
0.05 | 0.01 | -0.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.676 |
r_dihedral_angle_3_deg | 12.48 |
r_dihedral_angle_4_deg | 8.633 |
r_dihedral_angle_1_deg | 5.777 |
r_scangle_it | 4.409 |
r_scbond_it | 3.134 |
r_mcangle_it | 1.855 |
r_angle_refined_deg | 1.341 |
r_mcbond_it | 1.325 |
r_nbtor_refined | 0.303 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3855 |
Nucleic Acid Atoms | |
Solvent Atoms | 333 |
Heterogen Atoms | 50 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALEPACK | data scaling |
CCP4I | phasing |