2J7V
Structure of PBP-A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1MF0 | PRE-ALIGNED STRUCTURES WITH PDB ENTRIES 1MF0, 1E25, 1BSG, 1ERM, 1I2S |
experimental model | PDB | 1E25 | PRE-ALIGNED STRUCTURES WITH PDB ENTRIES 1MF0, 1E25, 1BSG, 1ERM, 1I2S |
experimental model | PDB | 1BSG | PRE-ALIGNED STRUCTURES WITH PDB ENTRIES 1MF0, 1E25, 1BSG, 1ERM, 1I2S |
experimental model | PDB | 1ERM | PRE-ALIGNED STRUCTURES WITH PDB ENTRIES 1MF0, 1E25, 1BSG, 1ERM, 1I2S |
experimental model | PDB | 1I2S | PRE-ALIGNED STRUCTURES WITH PDB ENTRIES 1MF0, 1E25, 1BSG, 1ERM, 1I2S |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | HANGING DROP. PROTEIN 10 MG/ML. RESERVOIR 500 UL HEPES 0.1 M PH 7.5, PROLINE 0.2 M, PEG-3350 10% (W/V) AND NAN3 0.02% (W/V). DROP 1UL PROTEIN AND 1 UL RESERVOIR |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 87.79 | α = 90 |
b = 91.9 | β = 90 |
c = 147.27 | 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 | IMAGE PLATE | MARRESEARCH | MIRROR 1, FLAT PRE-MIRROR. MIRROR 2, BENT, VERTICALLY FOCUSSING | 2004-06-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7B | EMBL/DESY, HAMBURG | BW7B |
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 | 1.9 | 39.2 | 99.8 | 0.08 | 13.9 | 5.1 | 94191 | 28.5 |
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) | |||||||||||
1 | 1.9 | 1.95 | 99.7 | 0.42 | 3.8 | 5.1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | PRE-ALIGNED STRUCTURES WITH PDB ENTRIES 1MF0, 1E25, 1BSG, 1ERM, 1I2S | 1.9 | 39.2 | 89464 | 4726 | 99.8 | 0.174 | 0.172 | 0.213 | RANDOM | 20.09 |
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] | |
0.67 | -0.74 | 0.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.132 |
r_dihedral_angle_4_deg | 18.856 |
r_dihedral_angle_3_deg | 13.835 |
r_dihedral_angle_1_deg | 5.843 |
r_scangle_it | 3.272 |
r_scbond_it | 2.28 |
r_angle_refined_deg | 1.51 |
r_mcangle_it | 1.135 |
r_mcbond_it | 1.016 |
r_angle_other_deg | 0.996 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8255 |
Nucleic Acid Atoms | |
Solvent Atoms | 870 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |