1QAE
THE ACTIVE SITE OF SERRATIA ENDONUCLEASE CONTAINS A CONSERVED MAGNESIUM-WATER CLUSTER
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | Other | 1.4 ANGSTROM STRUCTURE OF THE SERRATIAL ENDONUCLEASE (CAI, MILLER AND KRAUSE) WITH WATER AND ALTERNATE SIDE CHAIN CONFORMERS REMOVED AND THE SIDE CHAINS FOR THE ACTIVE SITE RESIDUES ARG 57, HIS 89, ASN 199 AND GLU 127 OMITTED |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.2 | 277 | CRYSTALLIZATION METHOD: VAPOR DIFFUSION SITTING DROP CRYSTALLIZATION TEMPERATURE: 277 K CRYSTALLIZATION PH: 4.6 CRYSTALS WERE GROWN FROM PEG 3350, AMMONIUM SULFATE, SODIUM ACETATE, AND STORED IN A STABILIZATION SOLUTION CONTAINING 20% PEG 3000, 400mM GLYCINE, 40mM TRIS, PH8.2 (293 K), 20% PEG 3000, 10% PEG 400. THIS SOLUTION WAS EXCHANGED THREE TIMES TO MINIMIZE CARRY OVER FROM THE STORAGE SOLUTION. AFTER 3 DAYS IN THE MAGNESIUM STABILIZATION SOLUTION, THE CRYSTAL OF DIMENSION 0.4 X 0.4 X 0.3 MM**2 WAS MOUNTED IN A SILICONIZED SPECIAL GLASS CAPILLARY. , VAPOR DIFFUSION, SITTING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.57 | 52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 106.7 | α = 90 |
b = 74.5 | β = 90 |
c = 68.9 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 288 | DIFFRACTOMETER | ENRAF-NONIUS FAST | 1998-02-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 |
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 | 2.05 | 45 | 84.3 | 0.025 | 40.87 | 3.1 | 30574 | 6.6 |
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) | |||||||||||
2.05 | 2.1 | 20.4 | 0.045 | 18.9 | 1.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | THROUGHOUT | 1.4 ANGSTROM STRUCTURE OF THE SERRATIAL ENDONUCLEASE (CAI, MILLER AND KRAUSE) WITH WATER AND ALTERNATE SIDE CHAIN CONFORMERS REMOVED AND THE SIDE CHAINS FOR THE ACTIVE SITE RESIDUES ARG 57, HIS 89, ASN 199 AND GLU 127 OMITTED | 2.05 | 50 | 2 | 29209 | 1483 | 83 | 0.167 | 0.21 | RANDOM | 14.8 |
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 |
x_dihedral_angle_d | 26.6 |
x_scangle_it | 3.53 |
x_scbond_it | 2.32 |
x_mcangle_it | 1.83 |
x_angle_deg | 1.3 |
x_mcbond_it | 1.12 |
x_improper_angle_d | 0.61 |
x_bond_d | 0.005 |
x_bond_d_na | |
x_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3690 |
Nucleic Acid Atoms | |
Solvent Atoms | 251 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
MADNESS | data collection |
PROCOR | data scaling |
PROCOR | data reduction |
XSCALE | data scaling |
ARP/wARP | model building |
X-PLOR | model building |
X-PLOR | refinement |
MADNESS | data reduction |
X-PLOR | phasing |