Experiment: 7ERB

Crystal structure of human Biliverdin IX-beta reductase B with Ataluren (PTC)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HE5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291.15	1.9-2.0M Ammonium sulfate, 0.1M Bis-tris(pH 6.5)

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.423	α = 90
b = 117.338	β = 90
c = 82.045	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		2020-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 11C	0.97942	PAL/PLS	11C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.5	41.71	99.36	0.111	0.999	9.77	9.4		128178			10.78

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.555			0.4377	0.818

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	1HE5	1.5	41.71	1.4	128064	2004	99.3	0.1712	0.1708	0.171	0.1986	0.1991	20.74

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	12.5344
f_angle_d	1.4809
f_chiral_restr	0.0889
f_bond_d	0.0144
f_plane_restr	0.0097

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6212
Nucleic Acid Atoms
Solvent Atoms	994
Heterogen Atoms	306

Software

Software
Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	model building
PHENIX	refinement
PHASER	phasing