PDB 3h86 experiment details and validation ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

X-ray diffraction

Source organism: Methanococcus maripaludis

Resolution: 2.5Å

Reported R values:

R R_free R_work

0.18 0.23 0.18

Entry percentile scores

X-ray diffraction

Sample information

Author description:

Crystal structure of adenylate kinase from Methanococcus maripaludis

Source organism:

Methanococcus maripaludis

Expression system:

Escherichia coli

Validation information

Metric	Description
Bond angles in protein, DNA, RNA molecules	11 outlier(s) of 7968 (%)
Bond lengths in protein, DNA, RNA molecules	8 outlier(s) of 5912 (%)
Electron density fit in protein, DNA, RNA molecules	37 outlier(s) of 764 (%)
Ramachandran outliers in protein molecules	6 outlier(s) of 756 (%)
Sidechain rotamer outliers in protein molecules	44 outlier(s) of 648 (%)

Experimental information

X-ray source:

RIGAKU RUH3R

Dataset statistics

Metric	Value	Source
Cell dimensions	a: 102.84 Å b: 102.84 Å c: 228.72 Å α: 90° β: 90° γ: 120°	Depositor
Number of reflections	31112	Xtriage(Phenix)
Test set size	10.02%	EDS
Data completeness	99.9%	EDS
EDS resolution	2.5Å - 19.7Å	EDS
<I/σ(I)>	2	Xtriage(Phenix)
Twinning statistics	<\|L\|> = 0.43 , <L²> = 0.26	Xtriage(Phenix)
Spacegroup	H 3	Depositor
Possible (pseudo-) translation	The largest off-origin peak in the Patterson function is 3.55% of the height of the origin peak. No significant pseudotranslation is detected.	Xtriage(Phenix)
Wilson B	56 Å²	Xtriage(Phenix)

Refinement statistics

Metric	Value	Source
Refinement software	REFMAC	DCC
Bulk solvent B	33 Å²	EDS
Bulk solvent k	0.33 e^-/Å³	EDS
Fo-Fc correlation	0.954	EDS
R value (DCC)	0.1839	DCC
R_free (DCC)	0.2066	DCC
R value (EDS)	0.1824	EDS

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3h86 @ RCSB
3h86 @ PDBj
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3h86 @ Proteopedia

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