3G46
Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloroform bound to the XE4 cavity
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 7.5 | 296 | 1.5-2.5M PHOSPHATE BUFFER, PH 7.50, SMALL TUBES, TEMPERATURE 298K, Microbatch, temperature 296K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.12 | 42 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 92.536 | α = 90 |
b = 43.487 | β = 122.25 |
c = 82.853 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 110 | CCD | ADSC QUANTUM 315 | 2005-11-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-BM-C | 0.9 | APS | 14-BM-C |
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 | 0.91 | 46.3 | 77.9 | 0.075 | 0.075 | 20 | 4 | 205646 | 160199 |
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) | ||||||||||
0.91 | 1.01 | 59.3 | 0.189 | 0.189 | 4.7 | 2.1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R | PDB ENTRY 3SDH | 0.91 | 46.3 | 152165 | 160199 | 8034 | 75.8 | 0.1288 | 0.1288 | 0.1288 | 0.1555 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
34 | 2315.44 | 2761.87 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_approx_iso_adps | 0.085 |
s_anti_bump_dis_restr | 0.046 |
s_similar_adp_cmpnt | 0.034 |
s_from_restr_planes | 0.0236 |
s_angle_d | 0.022 |
s_non_zero_chiral_vol | 0.016 |
s_zero_chiral_vol | 0.015 |
s_bond_d | 0.007 |
s_rigid_bond_adp_cmpnt | 0.005 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2424 |
Nucleic Acid Atoms | |
Solvent Atoms | 432 |
Heterogen Atoms | 98 |
Software
Software | |
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Software Name | Purpose |
SHELXL-97 | refinement |
CNS | refinement |
ADSC | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | phasing |