2H63 | pdb_00002h63

Crystal Structure of Human Biliverdin Reductase A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LC0	1LC0.pdb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	MgCl2, Bis-Tris, PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.787	α = 90
b = 92.747	β = 90
c = 147.755	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	CCD	MARMOSAIC 225 mm CCD		2006-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9789	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.7	41.3	96.8				33769

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.7	2.85	92.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1LC0.pdb	2.7	50	32324	32324	1399	96.42	0.23943	0.23943	0.23735	0.28	0.28691	0.33	RANDOM	57.219

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]
0.22			3.73		-3.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.486
r_dihedral_angle_3_deg	17.771
r_dihedral_angle_4_deg	14.491
r_dihedral_angle_1_deg	5.664
r_scangle_it	2.044
r_angle_refined_deg	1.514
r_scbond_it	1.265
r_angle_other_deg	0.954
r_mcangle_it	0.773
r_mcbond_it	0.438
r_nbd_refined	0.242
r_symmetry_vdw_refined	0.196
r_nbtor_refined	0.195
r_nbd_other	0.192
r_symmetry_vdw_other	0.185
r_xyhbond_nbd_refined	0.148
r_mcbond_other	0.121
r_nbtor_other	0.09
r_chiral_restr	0.081
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8453
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	192

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
CCP4	data scaling
PHASER	phasing