5HPG
STRUCTURE AND LIGAND DETERMINANTS OF THE RECOMBINANT KRINGLE 5 DOMAIN OF HUMAN PLASMINOGEN
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1PKR | PDB ENTRY 1PKR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | 24% (W/V) PEG 8000, 0.1 M NA-HEPES, PH 7.0, 0.15 M LI2(SO4) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.51 | 42 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.43 | α = 90 |
b = 79.2 | β = 90 |
c = 30.78 | γ = 90 |
Symmetry | |
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Space Group | P 21 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 | 123 | IMAGE PLATE | RIGAKU RAXIS II | MSC-YALE MIRRORS | 1997-04-04 | M |
Radiation Source | |||||
---|---|---|---|---|---|
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) | 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 | 1.66 | 35.26 | 72 | 0.042 | 0.051 | 14 | 2.5 | 16720 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.6 | 1.86 | 37 | 0.087 | 0.13 | 3.6 | 2.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 1PKR | 1.66 | 7 | 1 | 16720 | 15014 | 84 | 0.166 | 15.4 |
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 |
p_transverse_tor | 22.4 |
p_staggered_tor | 17.8 |
p_planar_tor | 5.2 |
p_multtor_nbd | 0.24 |
p_xyhbond_nbd | 0.23 |
p_singtor_nbd | 0.18 |
p_chiral_restr | 0.16 |
p_planar_d | 0.05 |
p_angle_d | 0.034 |
p_bond_d | 0.016 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1296 |
Nucleic Acid Atoms | |
Solvent Atoms | 193 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
RIGAKU | data collection |
RIGAKU | data reduction |
AMoRE | phasing |
PROFFT | refinement |
R-AXIS | data reduction |
R-AXIS | data scaling |