6YX8 | pdb_00006yx8

The structure of allophycocyanin from cyanobacterium Nostoc sp. WR13, the C2221 crystal form.

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YX7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	Morpheus screen condition E12: 37.5% v/v Precipitant mix 4: 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350; 0.1M Buffer system 3: 1.0M Tris (base); bicine, pH 8.5 0.12M Additives: 0.3M ethylene glycols

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.676	α = 90
b = 177.34	β = 90
c = 122.416	γ = 90

Symmetry
Space Group	C 2 2 21

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		2018-09-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

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	1.831	90.144	95.7	0.126	0.137	0.053	0.996	9.3	6.6		87249			26.15

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	1.831	1.941	58.3		1.278	1.278	0.524	0.599	1.5

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	6YX7	1.831	90.144	87257	4339	87.265	0.161	0.1595	0.17	0.1983	0.21	32.791

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]
0.262			-0.452		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.274
r_dihedral_angle_4_deg	18.567
r_dihedral_angle_3_deg	14.545
r_dihedral_angle_other_3_deg	13.127
r_lrange_it	6.711
r_lrange_other	6.338
r_dihedral_angle_1_deg	5.18
r_scangle_it	4.005
r_scangle_other	4.005
r_mcangle_other	2.558
r_mcangle_it	2.556
r_scbond_it	2.521
r_scbond_other	2.521
r_mcbond_it	1.749
r_mcbond_other	1.745
r_angle_refined_deg	1.547
r_angle_other_deg	1.351
r_nbd_other	0.255
r_symmetry_xyhbond_nbd_refined	0.255
r_symmetry_nbd_refined	0.239
r_xyhbond_nbd_other	0.224
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.208
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.162
r_symmetry_xyhbond_nbd_other	0.135
r_ncsr_local_group_6	0.111
r_ncsr_local_group_5	0.102
r_ncsr_local_group_1	0.099
r_ncsr_local_group_4	0.096
r_ncsr_local_group_2	0.095
r_ncsr_local_group_3	0.092
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7224
Nucleic Acid Atoms
Solvent Atoms	928
Heterogen Atoms	936

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
autoPROC	data scaling
STARANISO	data scaling
PHASER	phasing
Coot	model building