13DZ

X-ray crystal structure of human biliverdin beta IX reductase in complex with NADP and BCT002104

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 17-ID-1
Synchrotron site	NSLS-II
Beamline	17-ID-1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-05-25
Detector	DECTRIS EIGER X 9M
Wavelength(s)	0.9201
Spacegroup name	C 1 2 1
Unit cell lengths	76.156, 42.385, 66.738
Unit cell angles	90.00, 107.41, 90.00

Refinement procedure

Resolution	31.840 - 1.720
R-factor	0.1962
Rwork	0.195
R-free	0.22070
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.006
RMSD bond angle	1.083
Data reduction software	autoPROC
Data scaling software	autoPROC
Phasing software	PHASER
Refinement software	PHENIX (1.20.1_4487)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	31.841	1.754
High resolution limit [Å]	1.720	1.725
Rmerge	0.130	1.492
Rmeas	0.152	1.774
Rpim	0.078	0.948
Number of reflections	21585	1091
<I/σ(I)>	6.1	0.9
Completeness [%]	99.8	100
Redundancy	3.8	3.4
CC(1/2)	0.995	0.343

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	protein solution: BLVRB at 18 mg/mL in 50 mM Bis-Tris, pH 6.5, 50 mM NaCl, 1 mM DTT, 1 mM NADP+ well solution: 0.1 M MES monohydrate pH 6.5, 10-12% (w/v) PEG 20,000, and 25% (v/v) MPD. Crystallization droplets comprised 0.5 uL protein solution was mixed with 0.5 uL of well solution. BLVRB/NADP+ crystals were soaked for approximately 1 hour in a drop containing 2.5-5 mM BCT2104 (dissolved in 100% DMSO) and vitrified with 30% (v/v) glycerol as cryoprotectant.