4NLA
Structure of the central NEAT domain, N2, of the listerial Hbp2 protein, apo form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3SZ6 | PDB ENTRY 3SZ6 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 5.4 | 298 | 100 mM sodium citrate tribasic dihydrate, 200 mM potassium sodium tartrate tetrahydrate, 2.0 M ammonium sulfate, pH 5.4, vapor diffusion, temperature 298K, EVAPORATION |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.19 | 43.85 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.3 | α = 90 |
b = 89.3 | β = 90 |
c = 89.3 | γ = 90 |
Symmetry | |
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Space Group | I 2 3 |
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 | PIXEL | DECTRIS PILATUS 6M | MIRRORS. BENT CYLINDERS, STRIPES OF PT, RH AND CLEAR. | 2013-06-06 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.97950, 0.9686, 1.5418 | APS | 24-ID-C |
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 | 2.7 | 63.14 | 100 | 0.052 | 35.3 | 21.4 | 3370 | -3 | 109.36 |
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 | 2.7 | 2.85 | 100 | 0.471 | 6.3 | 22.8 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MAD | THROUGHOUT | PDB ENTRY 3SZ6 | 2.7 | 63.14 | 5408 | 3370 | 337 | 100 | 0.258 | 0.254 | 0.293 | RANDOM | 120.65 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 19.66 |
t_omega_torsion | 1.79 |
t_angle_deg | 1.02 |
t_bond_d | 0.008 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 947 |
Nucleic Acid Atoms | |
Solvent Atoms | 9 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
MLPHARE | phasing |
DM | phasing |
BUSTER-TNT | refinement |
PDB_EXTRACT | data extraction |
XSCALE | data scaling |
BUSTER | refinement |