6XWK | pdb_00006xwk

Crystal structure of Phormidium rubidum phycocyanin

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	MPD, PEG1000, PEG3350, Diethylene glycol, Triethylene glycol, Tetraethylene glycol, Pentaethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.32	α = 90
b = 106.32	β = 90
c = 58.67	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 PILATUS 6M-F		2016-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.84920	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.17	39.39	100	1	21.3	14		127070

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.17	1.2			0.51

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	4yjj	1.17	39.39	127046	6165	99.973	0.12	0.1188	0.12	0.145	0.15	15.305

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]
-0.981	-0.491		-0.981		3.184

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.319
r_dihedral_angle_other_3_deg	33.699
r_dihedral_angle_4_deg	20.377
r_dihedral_angle_3_deg	12.875
r_dihedral_angle_1_deg	4.83
r_rigid_bond_restr	4.404
r_lrange_it	3.81
r_lrange_other	3.15
r_scangle_other	3.127
r_scangle_it	3.126
r_scbond_it	2.454
r_scbond_other	2.453
r_mcangle_it	1.853
r_mcangle_other	1.833
r_angle_refined_deg	1.747
r_angle_other_deg	1.71
r_mcbond_it	1.58
r_mcbond_other	1.56
r_symmetry_nbd_refined	0.307
r_nbd_other	0.279
r_nbd_refined	0.231
r_symmetry_xyhbond_nbd_refined	0.202
r_symmetry_nbd_other	0.186
r_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_other	0.131
r_chiral_restr	0.101
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2484
Nucleic Acid Atoms
Solvent Atoms	463
Heterogen Atoms	190

Software

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