8PZK | pdb_00008pzk

Crystal structure of the Orange Carotenoid Protein 2 (OCP2) from Gloeocapsa sp. PCC 7428

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5TUX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		288	0.2 M Magnesium formate dihydrate, 0.1 M Sodium acetate trihydrate pH 4.0, 18% w/v Polyethylene glycol monomethyl ether 5,000

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.661	α = 90
b = 52.661	β = 90
c = 216.831	γ = 90

Symmetry
Space Group	P 43 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 EIGER X 16M		2023-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17B1	0.97920	SSRF	BL17B1

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	1.8	72.28	98.2	0.134	0.153	0.072	0.996	6.6	4.3		29081

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	1.8	1.83		92.3	2.668	3.031	1.414	0.283		4.4

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 (All)	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	1.8	54.208	28909	1498	98.043	0.2	0.1974	0.21	0.2481	0.25	RANDOM	33.141

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]
0.668			0.668		-1.337

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.282
r_dihedral_angle_3_deg	16.2
r_dihedral_angle_2_deg	13.96
r_dihedral_angle_1_deg	7.12
r_lrange_other	6.986
r_lrange_it	6.979
r_scangle_it	5.233
r_scangle_other	5.22
r_scbond_it	3.599
r_scbond_other	3.561
r_mcangle_other	3.445
r_mcangle_it	3.442
r_mcbond_it	2.35
r_mcbond_other	2.347
r_angle_refined_deg	1.819
r_angle_other_deg	0.674
r_nbd_refined	0.211
r_symmetry_nbd_refined	0.211
r_nbtor_refined	0.175
r_symmetry_nbd_other	0.161
r_xyhbond_nbd_refined	0.136
r_nbd_other	0.117
r_symmetry_xyhbond_nbd_refined	0.112
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2340
Nucleic Acid Atoms
Solvent Atoms	96
Heterogen Atoms	70

Software

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