2JDW
CRYSTAL STRUCTURE AND MECHANISM OF L-ARGININE: GLYCINE AMIDINOTRANSFERASE: A MITOCHONDRIAL ENZYME INVOLVED IN CREATINE BIOSYNTHESIS
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1JDW | PDB ENTRY 1JDW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | 1 PART OF AT38H (13-16 MG/ML) 2 PARTS OF PRECIPITANT (3% PEG 6000, 40 MM HEPES, 1MM GLUTATHIONE, PH7.0), SEVERAL DAYS AT ROOM TEMPERATURE, MACRO SEEDING. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.8 | 65 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 83.6 | α = 90 |
b = 83.6 | β = 90 |
c = 200.4 | γ = 90 |
Symmetry | |
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Space Group | P 43 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 | 290 | IMAGE PLATE | MARRESEARCH | 1995-11-16 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH2R |
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 | 2.1 | 8 | 97.6 | 0.087 | 3.19 | 40478 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
2.1 | 2.12 | 96.1 | 0.424 | 2.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | ISOMORPHOUS WITH PDB ENTRY 1JDW | PDB ENTRY 1JDW | 2.1 | 8 | 40478 | 97.6 | 0.199 | 0.199 | 26.22 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 24.96 |
x_angle_deg | 1.601 |
x_improper_angle_d | 1.45 |
x_bond_d | 0.011 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d | |
x_angle_d_na | |
x_angle_d_prot | |
x_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2940 |
Nucleic Acid Atoms | |
Solvent Atoms | 195 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
X-PLOR | model building |
X-PLOR | refinement |
MOSFLM | data reduction |
CCP4 | data scaling |
ROTAVATA | data scaling |
X-PLOR | phasing |