1X9F
Hemoglobin Dodecamer from Lumbricus Erythrocruorin
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.8 | 281 | 2.8M Na phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 281.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.92 | 57.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 139.225 | α = 90 |
b = 172.071 | β = 90 |
c = 202.886 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | IMAGE PLATE | RIGAKU RAXIS IIC | M | SINGLE WAVELENGTH | ||||||||
2 | 1 | x-ray | CCD | ADSC QUANTUM 4 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200H | 1.5418 | ||
2 | SYNCHROTRON | APS BEAMLINE 14-BM-C | 1.0000 | APS | 14-BM-C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.6 | 105.41 | 74920 | 74920 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3.8 Structure of the whole molecule | 2.6 | 105.41 | 74920 | 63085 | 3337 | 88.66 | 0.21481 | 0.21481 | 0.21316 | 0.24615 | RANDOM | 34.318 |
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] | |
-1.45 | -0.87 | 2.32 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.027 |
r_dihedral_angle_4_deg | 22.066 |
r_dihedral_angle_3_deg | 17.11 |
r_dihedral_angle_1_deg | 4.236 |
r_angle_refined_deg | 1.875 |
r_nbtor_refined | 0.304 |
r_nbd_refined | 0.297 |
r_symmetry_vdw_refined | 0.287 |
r_metal_ion_refined | 0.201 |
r_symmetry_hbond_refined | 0.201 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14028 |
Nucleic Acid Atoms | |
Solvent Atoms | 264 |
Heterogen Atoms | 555 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CNS | refinement |
SCALEPACK | data scaling |
CNS | phasing |