6IHD
Crystal structure of Malate dehydrogenase from Metallosphaera sedula
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293 | 35 %(v/v) 2-ethoxyethanol, 0.1M sodium cacodylate / hydrochloric acid pH 6.0 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.36 | 63.34 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 87.9 | α = 90 |
| b = 87.9 | β = 90 |
| c = 231.146 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 21 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 | ADSC QUANTUM 270 | 2017-02-28 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PAL/PLS BEAMLINE 7A (6B, 6C1) | 0.97934 | PAL/PLS | 7A (6B, 6C1) |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.3 | 50 | 97.7 | 0.075 | 0.078 | 0.02 | 15.3 | 11.3 | 40297 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 2.3 | 2.34 | 95.1 | 0.271 | 0.296 | 0.114 | 0.858 | 5.3 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution 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 | 4PLH | 2.3 | 50 | 38270 | 2006 | 97.78 | 0.1869 | 0.1841 | 0.2423 | RANDOM | 53.705 | |||||||
| 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] | |
| -0.03 | -0.03 | 0.06 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 41.637 |
| r_dihedral_angle_4_deg | 19.217 |
| r_dihedral_angle_3_deg | 17.879 |
| r_dihedral_angle_1_deg | 7.23 |
| r_angle_refined_deg | 1.941 |
| r_angle_other_deg | 1.076 |
| r_chiral_restr | 0.107 |
| r_bond_refined_d | 0.016 |
| r_gen_planes_refined | 0.008 |
| r_bond_other_d | 0.002 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4630 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 64 |
| Heterogen Atoms | 100 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-2000 | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| MOLREP | phasing |
| HKL-2000 | data reduction |
