PDB 3be4 experiment details and validation ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

X-ray diffraction

Source organism: Cryptosporidium parvum Iowa II

Resolution: 1.6Å

Reported R values:

R R_free R_work

0.16 0.2 0.16

Entry percentile scores

X-ray diffraction

Sample information

Author description:

Crystal structure of Cryptosporidium parvum adenylate kinase cgd5_3360

Source organism:

Cryptosporidium parvum Iowa II

Expression system:

Escherichia coli

Validation information

Metric	Description
Bond angles in protein, DNA, RNA molecules	23 outlier(s) of 2361 (%)
Bond lengths in protein, DNA, RNA molecules	21 outlier(s) of 1750 (%)
Electron density fit in protein, DNA, RNA molecules	3 outlier(s) of 223 (%)
Sidechain rotamer outliers in protein molecules	8 outlier(s) of 188 (%)

Experimental information

X-ray source:

APS BEAMLINE 19-ID

Dataset statistics

Metric	Value	Source
Cell dimensions	a: 101.175 Å b: 101.175 Å c: 72.433 Å α: 90° β: 90° γ: 120°	Depositor
Number of reflections	36130	Xtriage(Phenix)
Test set size	5.02%	EDS
Data completeness	99%	EDS
EDS resolution	1.6Å - 19.37Å	EDS
<I/σ(I)>	3	Xtriage(Phenix)
Twinning statistics	<\|L\|> = 0.47 , <L²> = 0.3	Xtriage(Phenix)
Spacegroup	H 3	Depositor
Possible (pseudo-) translation	The largest off-origin peak in the Patterson function is 4.71% of the height of the origin peak. No significant pseudotranslation is detected.	Xtriage(Phenix)
Wilson B	19 Å²	Xtriage(Phenix)

Refinement statistics

Metric	Value	Source
Refinement software	REFMAC	DCC
Bulk solvent B	54 Å²	EDS
Bulk solvent k	0.37 e^-/Å³	EDS
Fo-Fc correlation	0.971	EDS
R value (DCC)	0.1613	DCC
R_free (DCC)	0.2006	DCC
R value (EDS)	0.1628	EDS

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