Experiment: 8ELL

Apo human biliverdin reductase beta (cryogenic)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HDO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1M MES pH 6.5, 1-4% PEG 20000. Equilibrated over 0.25-0.5 M NaCl. BLVRB 18 mg/mL.

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.187	α = 90
b = 45.668	β = 90
c = 104.213	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2022-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE 7B2	1.12710	CHESS	7B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.52	52.1	97.8	0.115	0.12	0.034	0.999	12	12.5		31069			14.34

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.52	1.57	92.5		1.027	1.085	0.338	0.743	1.4	10.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6OPL	1.52	52.1	1.34	31068	1561	97.67	0.1609	0.1595	0.1593	0.1875	0.1876	18.6

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.2595
f_angle_d	0.9746
f_chiral_restr	0.0657
f_plane_restr	0.0096
f_bond_d	0.0077

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1544
Nucleic Acid Atoms
Solvent Atoms	325
Heterogen Atoms	2

Software

Software
Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
MOLREP	phasing