4CZC

Crystal structure of the siroheme decarboxylase NirDL in co-complex with iron-uroporphyrin III analogue

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	ROTATING ANODE
Temperature [K]	100
Detector technology	CCD
Collection date	2012-09-26
Detector	RIGAKU SATURN 944PLUS
Spacegroup name	C 1 2 1
Unit cell lengths	103.750, 72.600, 51.110
Unit cell angles	90.00, 102.06, 90.00

Refinement procedure

Resolution	28.680 - 2.900
R-factor	0.23215
Rwork	0.229
R-free	0.28432
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	4ch7
RMSD bond length	0.010
RMSD bond angle	1.657
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHASER
Refinement software	REFMAC (5.7.0032)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	28.700	2.980
High resolution limit [Å]	2.900	2.900
Rmerge	0.040	0.440
Number of reflections	8137
<I/σ(I)>	22.7	2.57
Completeness [%]	97.8	92.6
Redundancy	3.1	2.8

Crystallization Conditions

crystal ID	method	pH	temperature	details
1				FOR THE CRYSTALLIZATION OF THE NIRDL-FE-URO III CO-COMPLEX, NIRDL (7 MG/ML) WAS INCUBATED 30 MIN ON ICE WITH 0.5 MM FE-URO III (DISSOLVED IN 50 % DMSO) PRIOR TO CRYSTAL SETUP. PROTEIN-FE-URO III WAS MIXED WITH EQUAL AMOUNTS OF PRECIPITANT SOLUTION (27 % (V/V) MPD, 0.1 M MES, PH 5.5, AND 9.95 MM SPERMIDINE). CRYSTALS WERE CRYO-PROTECTED WITH 25-33 % (V/V) GLYCEROL OR ADDITIONAL 33 % (V/V) MPD PRIOR TO FLASH FREEZING IN LIQUID NITROGEN.