3I8U

Crystal structure of PcyA-181,182-dihydrobiliverdin complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.85M sodium citrate, 0.1M sodium cacodylate (pH 7.0), vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.822	α = 90
b = 95.087	β = 90
c = 42.782	γ = 90

Symmetry
Space Group	P 21 21 2

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	ADSC QUANTUM 315		2007-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0000	SPring-8	BL41XU

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	1.48	35.42	95.3	0.066		3.5		46254

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)
	1.48	1.56	97.9		0.307		3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	DIFFERENCE FOURIER	THROUGHOUT	2D1E	1.48	35.42	46226	2341	94.44	0.166	0.164	0.197	RANDOM	19.449

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
r_dihedral_angle_2_deg	36.609
r_dihedral_angle_4_deg	15.843
r_dihedral_angle_3_deg	13.819
r_dihedral_angle_1_deg	6.209
r_scangle_it	3.587
r_scbond_it	2.463
r_angle_refined_deg	1.901
r_mcangle_it	1.501
r_mcbond_it	1.322
r_angle_other_deg	1.125
r_mcbond_other	0.256
r_symmetry_vdw_other	0.246
r_nbd_refined	0.219
r_nbd_other	0.203
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.171
r_symmetry_hbond_refined	0.17
r_symmetry_vdw_refined	0.152
r_chiral_restr	0.09
r_nbtor_other	0.089
r_gen_planes_other	0.02
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2066
Nucleic Acid Atoms
Solvent Atoms	304
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling