6YX7

The high resolution structure of allophycocyanin from cyanobacterium Nostoc sp. WR13, the P21212 crystal form.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B33

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	Morpheus screen condition H12: Precipitant mix 4: 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350; Buffer system 3: 1.0M Tris (base); bicine, pH 8.5 Additives: amino acids: 0.2M Gly, DL-Ala, DL-Ser, DL-Glu, DL-Lys

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.695	α = 90
b = 177.726	β = 90
c = 106.372	γ = 90

Symmetry
Space Group	P 21 21 2

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		2018-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97932	Diamond	I03

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	1.419	106.372	96.1	0.077	0.082	0.027	0.998	13.8	8.7		383047			19.64

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	1.419	1.503	61.3		1.22	1.313	0.478	0.623	1.7	7.2

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1B33	1.419	106.372	383047	19133	87.258	0.128	0.1255	0.1751	25.715

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]
1.04			2.665		-3.705

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.912
r_dihedral_angle_other_3_deg	30.531
r_dihedral_angle_4_deg	15.71
r_dihedral_angle_3_deg	13.745
r_lrange_it	5.396
r_dihedral_angle_1_deg	4.856
r_lrange_other	4.683
r_scangle_it	3.961
r_scangle_other	3.961
r_scbond_it	3.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.912
r_dihedral_angle_other_3_deg	30.531
r_dihedral_angle_4_deg	15.71
r_dihedral_angle_3_deg	13.745
r_lrange_it	5.396
r_dihedral_angle_1_deg	4.856
r_lrange_other	4.683
r_scangle_it	3.961
r_scangle_other	3.961
r_scbond_it	3.3
r_scbond_other	3.3
r_mcangle_it	2.914
r_mcangle_other	2.914
r_rigid_bond_restr	2.503
r_mcbond_it	2.392
r_mcbond_other	2.392
r_angle_refined_deg	1.517
r_angle_other_deg	1.489
r_symmetry_nbd_refined	0.262
r_nbd_refined	0.218
r_nbd_other	0.214
r_symmetry_xyhbond_nbd_refined	0.196
r_symmetry_nbd_other	0.182
r_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.169
r_symmetry_xyhbond_nbd_other	0.123
r_ncsr_local_group_26	0.113
r_ncsr_local_group_3	0.111
r_ncsr_local_group_4	0.11
r_ncsr_local_group_14	0.108
r_ncsr_local_group_29	0.108
r_ncsr_local_group_13	0.106
r_ncsr_local_group_21	0.104
r_ncsr_local_group_19	0.103
r_ncsr_local_group_18	0.102
r_ncsr_local_group_25	0.102
r_ncsr_local_group_17	0.098
r_ncsr_local_group_15	0.097
r_ncsr_local_group_2	0.096
r_ncsr_local_group_28	0.096
r_ncsr_local_group_11	0.095
r_ncsr_local_group_6	0.094
r_ncsr_local_group_20	0.094
r_ncsr_local_group_27	0.094
r_ncsr_local_group_5	0.093
r_ncsr_local_group_12	0.093
r_ncsr_local_group_1	0.092
r_ncsr_local_group_8	0.09
r_ncsr_local_group_7	0.089
r_ncsr_local_group_9	0.087
r_ncsr_local_group_16	0.087
r_ncsr_local_group_30	0.087
r_chiral_restr	0.084
r_ncsr_local_group_24	0.084
r_symmetry_nbtor_other	0.083
r_ncsr_local_group_22	0.08
r_ncsr_local_group_10	0.075
r_ncsr_local_group_23	0.064
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.002