PDB 5o9q experiment details and validation ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

X-ray diffraction

Source organism: Saccharomyces cerevisiae S288C

Resolution: 1.4Å

Reported R values:

R R_free R_work

0.21 0.22 0.21

wwPDB Validation report is not available for this entry.

X-ray diffraction

Sample information

Author description:

Crystal structure of ScGas2 in complex with compound 6

Source organism:

Saccharomyces cerevisiae S288C

Expression system:

Komagataella pastoris

Validation information

Metric	Description
Bond angles in protein, DNA, RNA molecules	0 outlier(s) of 4783 (%)
Bond lengths in protein, DNA, RNA molecules	0 outlier(s) of 3539 (%)
Electron density fit in protein, DNA, RNA molecules	59 outlier(s) of 434 (%)
Ramachandran outliers in protein molecules	1 outlier(s) of 421 (%)
Sidechain rotamer outliers in protein molecules	5 outlier(s) of 380 (%)

Experimental information

X-ray source:

ALBA BEAMLINE XALOC

Dataset statistics

Metric	Value	Source
Cell dimensions	a: 49.963 Å b: 70.508 Å c: 150.585 Å α: 90° β: 90° γ: 90°	Depositor
Number of reflections	105292	Xtriage(Phenix)
Test set size	2.76%	EDS
Data completeness	99.8%	EDS
EDS resolution	1.4Å - 19.96Å	EDS
<I/σ(I)>	3.8	Xtriage(Phenix)
Twinning statistics	<\|L\|> = 0.47 , <L²> = 0.3	Xtriage(Phenix)
Spacegroup	P 2₁ 2₁ 2₁	Depositor
Possible (pseudo-) translation	The largest off-origin peak in the Patterson function is 5.27% of the height of the origin peak. No significant pseudotranslation is detected.	Xtriage(Phenix)
Wilson B	15 Å²	Xtriage(Phenix)

Refinement statistics

Metric	Value	Source
Refinement software	REFMAC	DCC
Bulk solvent B	41 Å²	EDS
Bulk solvent k	0.4 e^-/Å³	EDS
Fo-Fc correlation	0.949	EDS
R value (DCC)	0.2178	DCC
R_free (DCC)	0.2246	DCC
R value (EDS)	0.2171	EDS

Quick links

View

Close

Archive mmCIF file
Updated mmCIF file
PDB file
PDB header
Assembly composition XML
FASTA (Entry)
Summary report (PDF)
Full report (PDF)
Percentile plot (PNG)
Percentile plot (SVG)

5o9q @ RCSB
5o9q @ PDBj
5o9q @ PDBSum
5o9q @ Proteopedia

Downloads

Close

Archive mmCIF file
Updated mmCIF file
PDB file
PDB header
PDB file (gz)
PDBML
PDBML (ATOM lines)
PDBML (no atoms)
Structure Factors
EDS map
EDS difference map
Assembly composition XML
Assembly 1 (mmCIF; gz)
Assembly 1 (atom only; mmCIF)
FASTA (Entry)
SIFTS XML file with residue-level mappings
Summary report (PDF)
Full report (PDF)
Percentile plot (PNG)
Percentile plot (SVG)
Validation data (XML)

3D Visualisation

Links and resources