4GNO
Structure of rat cytosolic PEPCK Ld_3g in complex with Beta-Sulfopyruvate and GTP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3DT7 | PDB ENTRY 3DT7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.4 | 298 | 22-26% PEG3350, 0.1 M HEPES, pH 7.4, 10 mM manganese chloride, 10 mM GTP, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.21 | 44.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.792 | α = 90 |
b = 84.111 | β = 90 |
c = 118.564 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | ADSC QUANTUM 315r | Flat mirror (vertical focusing), single crystal Si(111) bent monochromator (horizontal focusing) | 2011-03-02 | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL7-1 | 0.9 | SSRL | BL7-1 |
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 | 1.5 | 100 | 93.8 | 0.06 | 16 | 4.5 | 91864 |
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 | 1.5 | 1.55 | 86.4 | 0.526 | 4.4 | 8347 |
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 | PDB ENTRY 3DT7 | 1.5 | 34.3 | 91525 | 4574 | 93.49 | 0.1686 | 0.1672 | 0.1944 | RANDOM | 18.3125 |
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] | |
-0.01 | 0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.352 |
r_dihedral_angle_4_deg | 14.271 |
r_dihedral_angle_3_deg | 12.695 |
r_dihedral_angle_1_deg | 6.102 |
r_angle_refined_deg | 1.589 |
r_chiral_restr | 0.103 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4813 |
Nucleic Acid Atoms | |
Solvent Atoms | 711 |
Heterogen Atoms | 50 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
HKL-2000 | data reduction |