2XV7
Crystal structure of vascular endothelial growth factor D
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SLS BEAMLINE X06SA |
Synchrotron site | SLS |
Beamline | X06SA |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2010-05-24 |
Detector | DECTRIS PILATUS 6M |
Spacegroup name | P 61 2 2 |
Unit cell lengths | 95.720, 95.720, 70.940 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 19.893 - 2.900 |
R-factor | 0.2626 |
Rwork | 0.255 |
R-free | 0.33250 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | VEGF-C FROM PDB ENTRY 2X1W |
RMSD bond length | 0.010 |
RMSD bond angle | 1.543 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | MOLREP |
Refinement software | PHENIX ((PHENIX.REFINE)) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 80.000 | 3.050 |
High resolution limit [Å] | 2.900 | 2.900 |
Rmerge | 0.090 | 0.770 |
Number of reflections | 36742 | |
<I/σ(I)> | 18 | 3.8 |
Completeness [%] | 99.7 | 99.7 |
Redundancy | 8.8 | 9.2 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | 4.2 | A SINGLE VEGF-D CRYSTAL GREW IN 6 WEEKS AT ROOM TEMPERATURE OVER A RESERVOIR SOLUTION OF 0.1 M PHOSPHATE/CITRATE BUFFER AT PH 4.2, 40 % ETHANOL (V/V), 5 % PEG 1000 (W/V). |