3FWY
Crystal structure of the L protein of Rhodobacter sphaeroides light-independent protochlorophyllide reductase (BchL) with MgADP bound: a homologue of the nitrogenase Fe protein
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2NIP | PDB ENTRY 2NIP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | CAPILLARY BATCH DIFFUSION | 7.8 | 301 | 20-25% PEG 3350, 200mM Magnesium formate, 10mM MgADP, pH 7.8, CAPILLARY BATCH DIFFUSION, temperature 301K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.01 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.729 | α = 90 |
b = 86.622 | β = 90 |
c = 117.169 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 100 | CCD | MARMOSAIC 325 mm CCD | Flat collimating mirror, toroid focusing mirror | 2008-01-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.98000 | SSRL | BL9-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.63 | 50 | 96.4 | 0.037 | 40 | 2 | 133747 | 133747 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.63 | 1.67 | 93.83 | 0.242 | 4.6 | 2 | 13313 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2NIP | 1.63 | 33.02 | 1.63 | 66727 | 3544 | 96.24 | 0.17529 | 0.17403 | 0.18 | 0.1986 | 0.2 | RANDOM | 14.577 |
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] | |
-0.01 | 0.01 | -0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.46 |
r_dihedral_angle_4_deg | 17.812 |
r_dihedral_angle_3_deg | 11.914 |
r_dihedral_angle_1_deg | 6.144 |
r_scangle_it | 6.086 |
r_scbond_it | 4.595 |
r_mcangle_it | 1.758 |
r_mcbond_it | 1.434 |
r_angle_refined_deg | 1.206 |
r_angle_other_deg | 0.874 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4112 |
Nucleic Acid Atoms | |
Solvent Atoms | 402 |
Heterogen Atoms | 64 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |