3TH3
Mg2+ Is Required for Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors At Physiological Ca2+
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2A2Q | PDB ENTRY 2A2Q |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | 298 | 20% PEG 4000, 50 mM Tris-HCL, 50 mM N-(2-Acetamido)iminodiacetic acid, 150 mM NaCl, 2.5 mM Calcium Chloride, 1.25 mM Magnesium Chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.14 | 60.84 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 78.079 | ¦Á = 90 |
b = 68.894 | ¦Â = 91.19 |
c = 79.153 | ¦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 | 200 | CCD | ADSC QUANTUM 315 | 2006-09-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.2 | ALS | 8.2.2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.7 | 55.01 | 98.8 | 0.125 | 0.1 | 9.98 | 3.4 | 22917 | 2 |
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2A2Q | 2.7 | 55.01 | 2 | 21733 | 1184 | 98.4 | 0.232 | 0.228 | 0.298 | RANDOM | 47.43 |
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] | |
-0.02 | 0.02 | -0.04 | 0.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.103 |
r_dihedral_angle_3_deg | 21.821 |
r_dihedral_angle_4_deg | 15.934 |
r_dihedral_angle_1_deg | 7.45 |
r_scangle_it | 3.654 |
r_scbond_it | 2.172 |
r_angle_refined_deg | 1.85 |
r_mcangle_it | 1.596 |
r_mcbond_it | 0.83 |
r_chiral_restr | 0.108 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3934 |
Nucleic Acid Atoms | |
Solvent Atoms | 83 |
Heterogen Atoms | 65 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
AMoRE | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |