4IMR
Crystal structure of 3-oxoacyl (acyl-carrier-protein) reductase (target EFI-506442) from agrobacterium tumefaciens C58 with NADP bound
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4G81 | PDB ENTRY 4G81 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 6.5 | 0.1M SODIUM CACODYLATE, PH 6.5, 1M SODIUM CITRATE TRIBASIC, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.99 | 58.83 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 87.919 | α = 90 |
| b = 87.919 | β = 90 |
| c = 308.309 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 61 2 2 |
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 | RAYONIX MX225HE | MIRRORS | 2012-11-11 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 31-ID | APS | 31-ID | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.95 | 50 | 89.4 | 0.14 | 6.9 | 20.4 | 46926 | -3 | |||||||||||
| 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 | 1.95 | 1.98 | 100 | 0.65 | 4 | 21.6 | |||||||||||||
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 4G81 | 1.96 | 34.16 | 42648 | 1363 | 84.49 | 0.1819 | 0.18065 | 0.18 | 0.21908 | 0.22 | RANDOM | 22.404 | ||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
| 0.26 | 0.26 | 0.26 | -0.84 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 39.914 |
| r_dihedral_angle_4_deg | 18.56 |
| r_dihedral_angle_3_deg | 13.997 |
| r_dihedral_angle_1_deg | 5.521 |
| r_angle_refined_deg | 1.419 |
| r_chiral_restr | 0.089 |
| r_bond_refined_d | 0.009 |
| r_gen_planes_refined | 0.006 |
| r_bond_other_d | |
| r_angle_other_deg | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3749 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 380 |
| Heterogen Atoms | 105 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHASER | phasing |
| REFMAC | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
