8II8 | pdb_00008ii8

X-ray crystal structure of pink-colored protein from Pleurotus salmoneostramineus in complex with natural chromophore

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		artificial helices without side chain

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	293	PEG4000, sodium formate, Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.879	α = 90
b = 31.895	β = 95.939
c = 107.416	γ = 90

Symmetry
Space Group	I 1 2 1

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 EIGER X 16M		2022-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

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	1.25	30.56	99.1	0.071	0.098	0.068	0.99	9.4	3.4		54840

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	1.25	1.27	98.6		0.276	0.383	0.264	0.896	3.8	3.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	artificial helices without side chain	1.25	30.56	54839	2826	98.978	0.133	0.1311	0.13	0.1641	0.16	14.602

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]
0.684		0.017	-1.524		0.818

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.685
r_dihedral_angle_3_deg	12.751
r_dihedral_angle_2_deg	11.799
r_rigid_bond_restr	5.928
r_dihedral_angle_1_deg	4.183
r_lrange_it	3.566
r_lrange_other	3.236
r_scangle_it	3.106
r_scangle_other	3.105
r_scbond_other	2.519
r_scbond_it	2.518
r_angle_refined_deg	1.723
r_mcangle_other	1.587
r_mcangle_it	1.583
r_mcbond_it	1.215
r_mcbond_other	1.208
r_angle_other_deg	0.617
r_nbd_refined	0.259
r_nbd_other	0.222
r_symmetry_xyhbond_nbd_refined	0.192
r_nbtor_refined	0.185
r_symmetry_nbd_other	0.179
r_symmetry_nbd_refined	0.171
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.094
r_symmetry_nbtor_other	0.07
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1657
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing