3JQP
Crystal structure of the H286L mutant of Ferredoxin-NADP+ reductase from Plasmodium falciparum with 2'P-AMP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2OK7 | PDB ENTRY 2OK7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | Microbatch, permeable oil | 6.5 | 293 | 12% PEG 6000, 5% glycerol, 0.1 M cacodylate-NaOH , pH 6.5, Microbatch, permeable oil, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.59 | 52.55 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 122.57 | ¦Á = 90 |
b = 122.57 | ¦Â = 90 |
c = 133.744 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 31 |
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 | MARRESEARCH | 2008-10-07 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ELETTRA BEAMLINE 5.2R | ELETTRA | 5.2R |
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 | 2.8 | 56.58 | 100 | 0.157 | 9.5 | 3.9 | 44994 | 44994 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
3 | 3.16 | 99.9 | 0.775 | 1.7 | 3.7 | 6554 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | 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 | PDB ENTRY 2OK7 | 3 | 56.58 | 2 | 42693 | 42693 | 2268 | 99.96 | 0.24776 | 0.24776 | 0.24415 | 0.31661 | RANDOM | 55.833 |
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] | |
2.3 | 1.15 | 2.3 | -3.45 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.118 |
r_dihedral_angle_3_deg | 17.982 |
r_dihedral_angle_4_deg | 17.865 |
r_dihedral_angle_1_deg | 5.575 |
r_scangle_it | 2.773 |
r_mcangle_it | 1.914 |
r_scbond_it | 1.645 |
r_angle_refined_deg | 1.332 |
r_mcbond_it | 1.061 |
r_chiral_restr | 0.085 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13228 |
Nucleic Acid Atoms | |
Solvent Atoms | 166 |
Heterogen Atoms | 480 |
Software
Software | |
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Software Name | Purpose |
MOLREP | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |