1SDN
CRYSTAL STRUCTURE OF A DEACYLATION-DEFECTIVE MUTANT OF PENICILLIN-BINDING PROTEIN 5 MODIFIED BY MERCURY
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 294 | 24% (w/v) polyethylene glycol 8000, 50mM sodium citrate, 100mM magnesium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.77 | 55.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.7 | α = 90 |
b = 50.7 | β = 90 |
c = 140.3 | γ = 120 |
Symmetry | |
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Space Group | P 32 |
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 | 294 | IMAGE PLATE | MAC Science DIP-2000H | mirrors | 1998-08-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | ENRAF-NONIUS FR591 | 1.5418 |
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 | 2.5 | 25.4 | 95.6 | 0.074 | 11.2 | 2.53 | 13482 | 13482 | 30.1 |
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) | |||||||||||
2.5 | 2.59 | 88.7 | 0.203 | 4.4 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | REFINEMENT | THROUGHOUT | PDB ENTRY 1HD8 | 2.5 | 15 | 13044 | 13044 | 688 | 98.28 | 0.1744 | 0.17447 | 0.17113 | 0.24142 | RANDOM | 30.141 |
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] | |
-0.7 | -0.35 | -0.7 | 1.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 6.006 |
r_scangle_it | 3.267 |
r_scbond_it | 1.865 |
r_mcangle_it | 1.408 |
r_angle_refined_deg | 1.275 |
r_mcbond_it | 0.728 |
r_nbd_refined | 0.196 |
r_xyhbond_nbd_refined | 0.149 |
r_symmetry_vdw_refined | 0.14 |
r_symmetry_hbond_refined | 0.119 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2679 |
Nucleic Acid Atoms | |
Solvent Atoms | 46 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
NONIUS | data reduction |
SCALEPACK | data scaling |
CNS | phasing |