2J65
Structure of LpxC from Aquifex aeolicus in complex with UDP
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1P42 | PDB ENTRY 1P42 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | CRYSTALS OF LPXC WERE GROWN BY HANGING VAPOR DIFFUSION AT 20 DEG C USING 1 UL OF PROTEIN (184 UM) AND 1 UL OF A RESERVOIR SOLUTION CONTAINING 8% PEG 6000, 100 MM TRIS, PH 8.5, AND 300 MM NACL. |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.69 | 53.9 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 101.755 | α = 90 |
| b = 101.755 | β = 90 |
| c = 124.243 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 61 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | MARRESEARCH | PT-COATED MIRRORS, MICROFOCUS BEAMLINE | 2006-05-20 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | ESRF | ID23-2 | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 2.2 | 50.9 | 99 | 0.11 | 11.3 | 3.9 | 36577 | ||||||||||||
| 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 | 2.2 | 2.32 | 98.5 | 0.48 | 3.6 | 3.9 | |||||||||||||
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 (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 1P42 | 2.2 | 50.9 | 34736 | 1836 | 98.9 | 0.171 | 0.168 | 0.17 | 0.225 | 0.22 | RANDOM | 22.83 | ||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
| -0.86 | -0.43 | -0.86 | 1.28 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.024 |
| r_dihedral_angle_4_deg | 21.107 |
| r_dihedral_angle_3_deg | 14.182 |
| r_dihedral_angle_1_deg | 5.973 |
| r_scangle_it | 2.701 |
| r_scbond_it | 1.671 |
| r_angle_refined_deg | 1.34 |
| r_mcangle_it | 1.058 |
| r_mcbond_it | 0.653 |
| r_nbtor_refined | 0.3 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4314 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 488 |
| Heterogen Atoms | 107 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
