3MBG
Crystal Structure of Human Augmenter of Liver Regeneration (ALR)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1OQC | PDB ENTRY 1OQC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 298 | 18% w/v PEG 8000, 210 mM zinc acetate dihydrate, 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 112.719 | α = 90 |
b = 65.145 | β = 89.97 |
c = 63.767 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 93 | IMAGE PLATE | RIGAKU RAXIS IV | OSMIC BLUE OPTICS | 2009-08-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R |
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 | 1.85 | 63.76 | 99.9 | 0.044 | 36.54 | 3.6 | 49190 |
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) | |||||||||||
1.85 | 1.92 | 100 | 0.366 | 3.13 | 3.6 |
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 1OQC | 1.85 | 27.76 | 37427 | 1975 | 99.88 | 0.19129 | 0.18914 | 0.23121 | RANDOM | 29.797 |
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 |
r_dihedral_angle_2_deg | 32.027 |
r_dihedral_angle_3_deg | 13.022 |
r_dihedral_angle_4_deg | 12.403 |
r_dihedral_angle_1_deg | 5.196 |
r_scangle_it | 3.874 |
r_scbond_it | 2.338 |
r_angle_refined_deg | 1.889 |
r_mcangle_it | 1.648 |
r_mcbond_it | 0.905 |
r_symmetry_vdw_refined | 0.347 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2799 |
Nucleic Acid Atoms | |
Solvent Atoms | 291 |
Heterogen Atoms | 217 |
Software
Software | |
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Software Name | Purpose |
StructureStudio | data collection |
CCP4 | model building |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
ARP/wARP | model building |