6T6K | pdb_00006t6k

Y201W mutant of the orange carotenoid protein from Synechocystis at pH 6.5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XB5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	0.1M DL-Glutamic acid monohydrate; 0.1M DL-Alanine; 0.1M Glycine; 0.1M DL-Lysine monohydrochloride; 0.1M DL-Serine; 0.1M Imidazole; MES monohydrate (acid), pH 6.5; 20% v/v Ethylene glycol; 10 % w/v PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.726	α = 90
b = 82.726	β = 90
c = 88.044	γ = 120

Symmetry
Space Group	P 32 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		2019-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.976250	PETRA III, EMBL c/o DESY	P14 (MX2)

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	1.37	44.02	100	0.047	0.999	29.1	20.2		73479

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	1.37	1.39	100		1.532	0.816		20.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4XB5	1.37	37.54	69781	3654	99.93	0.1369	0.1354	0.15	0.1668	0.18	RANDOM	29.765

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]
0.7	0.35		0.7		-2.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.803
r_dihedral_angle_4_deg	20.265
r_rigid_bond_restr	16.467
r_dihedral_angle_3_deg	12.336
r_dihedral_angle_1_deg	5.766
r_angle_other_deg	1.526
r_angle_refined_deg	1.357
r_chiral_restr	0.078
r_bond_refined_d	0.007
r_bond_other_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2343
Nucleic Acid Atoms
Solvent Atoms	305
Heterogen Atoms	50

Software

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