8OR7 | pdb_00008or7

Structure of a far-red induced allophycocyanin from Chroococcidiopsis thermalis sp. PCC 7203

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4PO5
experimental model	PDB	1KN1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	289	0.5 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 1.0 M lithium sulfate monohydrate

Crystal Properties
Matthews coefficient	Solvent content
3.57	65.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.54	α = 90
b = 130.54	β = 90
c = 106.496	γ = 120

Symmetry
Space Group	P 63

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 EIGER2 S 9M		2022-01-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.97918	SSRF	BL02U1

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	2.57	77.52	100	0.091	1	20.3	18.5		32743

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	2.57	2.71	100		1.217	0.843	2.5	16.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.8	77.52	24255	1240	99.98	0.18093	0.17775	0.18	0.24016	0.24	RANDOM	75.646

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]
-0.17	-0.08		-0.17		0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	23.577
r_dihedral_angle_2_deg	15.249
r_long_range_B_refined	15.045
r_long_range_B_other	15.045
r_scangle_other	12.358
r_mcangle_it	10.2
r_mcangle_other	10.199
r_scbond_it	9.098
r_scbond_other	8.921
r_mcbond_it	7.63
r_mcbond_other	7.626
r_dihedral_angle_1_deg	4.776
r_angle_refined_deg	1.511
r_angle_other_deg	0.506
r_chiral_restr	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4986
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	191

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
pointless	data scaling
ARP/wARP	phasing