6XR5
Crystal Structure of Diphosphomevalonate decarboxylase (MVD1) Cryptococcus neoformans var. grubii serotype A
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 | 2018-04-12 |
Detector | RAYONIX MX-300 |
Wavelength(s) | 0.97872 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 95.510, 168.050, 101.210 |
Unit cell angles | 90.00, 90.14, 90.00 |
Refinement procedure
Resolution | 48.320 - 1.700 |
R-factor | 0.1564 |
Rwork | 0.156 |
R-free | 0.18160 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1j20 as per Morda |
RMSD bond length | 0.009 |
RMSD bond angle | 0.976 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | MoRDa |
Refinement software | PHENIX (1.18.2) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 48.320 | 48.320 | 1.740 |
High resolution limit [Å] | 1.700 | 7.600 | 1.700 |
Rmerge | 0.052 | 0.022 | 0.439 |
Rmeas | 0.060 | 0.026 | 0.530 |
Total number of observations | 1298519 | ||
Number of reflections | 347919 | 3958 | 25184 |
<I/σ(I)> | 16.05 | 40.79 | 2.39 |
Completeness [%] | 99.7 | 98.5 | 97.6 |
Redundancy | 3.732 | 3.707 | 3.132 |
CC(1/2) | 0.999 | 0.999 | 0.824 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 287 | igaku Reagents MCSG1 screen D1: 200mM ammonium sulfate, 25% (w/V) PEG 3350, 100mM Bis-Tris / HCl pH 6.5: CrneC.18225.a.B1.PS38378 at 20.79mg/ml + 4mM AMPPNP / MgCl2:: tray: 297436d1 cryo: 15% EG: puck ihw4-7. |