2WX5
Hexa-coordination of a bacteriochlorophyll cofactor in the Rhodobacter sphaeroides reaction centre
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1AIG | PDB ENTRY 1AIG |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | MOTHER LIQUOR AT 9 MG/ML OF THE AM149W REACTION CENTRE, 0.09% V/V LDAO, 3.5% W/V HEPTANE-1, 2,3-TRIOL AND 0.65 M POTASSIUM PHOSPHATE (PH 8.0) WERE EQUILIBRATED AGAINST A RESERVOIR SOLUTION OF 1.5 M POTASSIUM PHOSPHATE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.6 | 78 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 140.18 | α = 90 |
b = 140.18 | β = 90 |
c = 185.401 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | 100 | 2004-11-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX14.1 | SRS | PX14.1 |
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 | 2.63 | 44.54 | 98.6 | 0.1 | 8.2 | 4.9 | 61876 |
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 | 2.63 | 2.78 | 94.9 | 0.7 | 1.5 | 4.1 |
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 1AIG | 2.63 | 20.4 | 58556 | 3126 | 98.49 | 0.23941 | 0.23728 | 0.27866 | RANDOM | 68.291 |
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] | |
1.29 | 0.64 | 1.29 | -1.93 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.59 |
r_dihedral_angle_4_deg | 21.238 |
r_dihedral_angle_3_deg | 18.394 |
r_scangle_it | 8.249 |
r_dihedral_angle_1_deg | 6.848 |
r_scbond_it | 5.833 |
r_mcangle_it | 4.388 |
r_mcbond_it | 2.536 |
r_angle_refined_deg | 2.223 |
r_chiral_restr | 0.118 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6469 |
Nucleic Acid Atoms | |
Solvent Atoms | 292 |
Heterogen Atoms | 707 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |