8CSO
Crystal Structure of Orotidine 5'-phosphate decarboxylase from Klebsiella pneumoniae in complex with Uridine-5'-monophosphate
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 21-ID-F |
Synchrotron site | APS |
Beamline | 21-ID-F |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2022-02-24 |
Detector | RAYONIX MX-300 |
Wavelength(s) | 0.97872 |
Spacegroup name | P 1 |
Unit cell lengths | 61.710, 91.310, 127.730 |
Unit cell angles | 100.94, 100.36, 91.11 |
Refinement procedure
Resolution | 48.340 - 2.600 |
R-factor | 0.1983 |
Rwork | 0.197 |
R-free | 0.23480 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1eix as per MoRDa |
RMSD bond length | 0.004 |
RMSD bond angle | 0.698 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | MoRDa |
Refinement software | PHENIX (1.20.1) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 2.670 |
High resolution limit [Å] | 2.600 | 11.630 | 2.600 |
Rmerge | 0.072 | 0.026 | 0.632 |
Rmeas | 0.084 | 0.030 | 0.731 |
Number of reflections | 81130 | 868 | 5990 |
<I/σ(I)> | 14.65 | 39.96 | 2.11 |
Completeness [%] | 98.0 | 93.2 | 97.5 |
Redundancy | 3.935 | 3.49 | 3.981 |
CC(1/2) | 0.998 | 0.999 | 0.768 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 287 | RigakuReagents JCSG Top96 screen, conditon D12: 1000mM sodium citrate tribasic, 100mM CHES/NaOH pH 9.5; KlpnC.01229.a.B1.PW39025 at 18mg/ml + 3m UMP; tray 322516 d12: cryo: 20% EG + 3mM UMP: puck dnf8-2. |