2HCI
Structure of Human Mip-3a Chemokine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1M8A | PDB ENTRY 1M8A |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 1.6M ammonium sulfate, 10% v/v dioxane, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.2 | 61.55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 83.991 | α = 90 |
b = 83.991 | β = 90 |
c = 57.221 | γ = 90 |
Symmetry | |
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Space Group | I 4 |
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 | SBC-2 | 2001-03-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 0.95370 | APS | 17-ID |
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 | 1.81 | 21.57 | 100 | 0.062 | 9.1 | 3.47 | 17465 |
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) | |||||||||||
1.81 | 1.99 | 16.6 | 100 | 0.3082 | 2.4 | 1.78 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 1M8A | 1.81 | 59.76 | 16315 | 16315 | 872 | 94.12 | 0.20944 | 0.2064 | 0.2545 | RANDOM | 27.793 |
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] | |
0.26 | 0.26 | -0.51 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_angle_refined_deg | 1.856 |
r_angle_other_deg | 0.955 |
r_symmetry_hbond_refined | 0.35 |
r_nbd_refined | 0.264 |
r_symmetry_vdw_refined | 0.23 |
r_nbd_other | 0.211 |
r_symmetry_vdw_other | 0.196 |
r_nbtor_refined | 0.191 |
r_chiral_restr | 0.13 |
r_nbtor_other | 0.094 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1059 |
Nucleic Acid Atoms | |
Solvent Atoms | 156 |
Heterogen Atoms | 21 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
d*TREK | data reduction |
AMoRE | phasing |
REFMAC | refinement |