1HE3 | pdb_00001he3

Human biliverdin IX beta reductase: NADP/mesobiliverdin IV alpha ternary complex

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		6.5		30% PEG 3350, 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE PH 6.5. NADP ADDED TO A FINAL CONCENTRATION OF 2.5 MM

Crystal Properties
Matthews coefficient	Solvent content
2.3	40.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.2	α = 90
b = 49.4	β = 90
c = 107.1	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				2000-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3		ESRF	ID14-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.4	44.7	98.6	0.08	4.1	3.8		42097

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.48	98.6		0.183

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1HDO	1.4	20	42030	2115	98.3	0.138	0.132		0.181	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
13		1860.38

RMS Deviations
Key	Refinement Restraint Deviation
s_approx_iso_adps	0.08
s_similar_adp_cmpnt	0.028
s_angle_d	0.027
s_non_zero_chiral_vol	0.027
s_from_restr_planes	0.026
s_zero_chiral_vol	0.019
s_anti_bump_dis_restr	0.015
s_bond_d	0.011
s_rigid_bond_adp_cmpnt	0.004
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1536
Nucleic Acid Atoms
Solvent Atoms	289
Heterogen Atoms	91

Software

Software
Software Name	Purpose
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.