1QK5
TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE WITH XMP, PYROPHOSPHATE AND TWO MG2+ IONS
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1QK3 | PDB ENTRY 1QK3, SUBUNIT A, WITHOUT LOOPS, WATERS, OR GMP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8.5 | 277 | 30% PEG 4000, 100 MM TRIS.CL (PH 8.5), 200 MM LI2SO4, 0.25 % BETA-OCTYLGLUCOPYRANOSIDE. THE CRYSTAL WAS GROWN IN THE PRESENCE OF 1 MM XANTHINE, 1 MM PRPP AND 10 MM MGCL2 AT 277 K. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.208 | α = 90 |
b = 112.255 | β = 90 |
c = 144.28 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | PRINCETON SCIENTIFIC INSTRUMENTS 2K CCD | PT-COATED MIRROR | 1998-02-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X25 | NSLS | X25 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.6 | 13 | 98 | 0.076 | 10.3 | 4.2 | 58200 | 24.14 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.6 | 1.66 | 93.9 | 0.373 | 2.4 | 3.7 |
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-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 1QK3, SUBUNIT A, WITHOUT LOOPS, WATERS, OR GMP | 1.6 | 13 | 55139 | 2953 | 98 | 0.23351 | 0.23 | 0.26099 | 0.26 | RANDOM | 25.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
p_scangle_it | 3.53 |
p_mcangle_it | 2.466 |
p_scbond_it | 2.282 |
p_mcbond_it | 1.709 |
p_chiral_restr | 0.147 |
p_angle_d | 0.04 |
p_planar_d | 0.038 |
p_bond_d | 0.015 |
p_plane_restr | 0.012 |
p_angle_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3472 |
Nucleic Acid Atoms | |
Solvent Atoms | 182 |
Heterogen Atoms | 70 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
AMoRE | phasing |