7YH4
Crystal structure of human cytosolic beta-alanyl lysine dipeptidase (PM20D2)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | RRCAT INDUS-2 BEAMLINE PX-BL21 |
Synchrotron site | RRCAT INDUS-2 |
Beamline | PX-BL21 |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2021-08-13 |
Detector | MARMOSAIC 225 mm CCD |
Wavelength(s) | 0.987 |
Spacegroup name | I 2 2 2 |
Unit cell lengths | 78.834, 112.888, 123.217 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 35.624 - 2.030 |
R-factor | 0.1989 |
Rwork | 0.197 |
R-free | 0.23680 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3ram |
RMSD bond length | 0.006 |
RMSD bond angle | 0.776 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | PHENIX ((1.14_3260: ???)) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 44.590 | 2.080 |
High resolution limit [Å] | 2.030 | 2.030 |
Rmerge | 0.049 | 1.140 |
Rmeas | 0.053 | |
Rpim | 0.020 | 0.540 |
Number of reflections | 35868 | 2616 |
<I/σ(I)> | 23.3 | 1.7 |
Completeness [%] | 100.0 | 99.8 |
Redundancy | 7.2 | 5.4 |
CC(1/2) | 1.000 | 0.690 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | MICROBATCH | 4.6 | 294 | 70 mM calcium chloride, 35 mM sodium acetate pH4.6, 7% isopropanol, 15% glycerol, 20mM Tris-Cl, 200 mM NaCl (mixed in 1:1) |