6BWR
LarC2, the C-terminal domain of a cyclometallase involved in the synthesis of the NPN cofactor of lactate racemase, in complex with nickel
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 21-ID-D |
Synchrotron site | APS |
Beamline | 21-ID-D |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2017-11-20 |
Detector | DECTRIS EIGER X 9M |
Wavelength(s) | 1.033 |
Spacegroup name | P 21 3 |
Unit cell lengths | 96.634, 96.634, 96.634 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 48.317 - 1.810 |
R-factor | 0.1616 |
Rwork | 0.138 |
R-free | 0.19190 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6bwo |
RMSD bond length | 0.009 |
RMSD bond angle | 0.937 |
Data reduction software | XDS (2.99) |
Data scaling software | Aimless (0.5.32) |
Phasing software | PHASER (2.8.0) |
Refinement software | PHENIX (1.12-2829) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 48.320 | 48.320 | 1.850 |
High resolution limit [Å] | 1.810 | 9.050 | 1.810 |
Rmerge | 0.079 | 0.030 | 1.109 |
Rmeas | 0.083 | 0.032 | 1.174 |
Rpim | 0.027 | 0.011 | 0.380 |
Total number of observations | 260115 | ||
Number of reflections | 27744 | 257 | 1665 |
<I/σ(I)> | 19.4 | ||
Completeness [%] | 99.9 | 98.4 | 99.7 |
Redundancy | 9.4 | 7.9 | 9.4 |
CC(1/2) | 0.999 | 0.999 | 0.537 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 294.15 | 0.5 ul ~5.5 mg/ml LarC (100 mM Tris-HCl pH 7.5, 300 mM NaCl) were mixed with 0.5 ul of reservoir solution. Hanging drop reservoir contained 100 ul of 0.2 M Lithium chloride, 0.1 M Tris pH 8.0, 20% w/v Polyethylene glycol 6,000. Crystal grew within two weeks. The crystal was soaked in 16 mM Nickel chloride + reservoir solution for 30 minutes and then for 1 minute in 20% Polyethylene glycol 400, 80% reservoir solution. |