8PYH | pdb_00008pyh

Crystal structure of the Orange Carotenoid Protein 2 (OCP2) from Crinalium epipsammum PCC 9333

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		288	0.1 M Imidazole pH 6.5, 1.0 M Sodium acetate trihydrate

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.054	α = 90
b = 103.727	β = 90
c = 109.62	γ = 90

Symmetry
Space Group	P 21 21 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	RIGAKU HyPix-6000HE		2023-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54184

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	2.2	22.2	99.7	0.13	0.14	0.051	0.993	12.3	7.5		35514

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	2.2	2.27		98.2	0.384	0.412	0.146	0.874		7.8

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	2.2	22.2	33599	1821	85.45	0.17991	0.17739	0.18	0.22693	0.23	RANDOM	18.65

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]
-7.07			14.17		-7.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.381
r_dihedral_angle_2_deg	15.798
r_dihedral_angle_1_deg	9.199
r_long_range_B_refined	6.3
r_long_range_B_other	6.3
r_scangle_other	3.919
r_mcangle_it	3.908
r_mcangle_other	3.908
r_scbond_it	2.591
r_scbond_other	2.591
r_mcbond_it	2.584
r_mcbond_other	2.579
r_angle_refined_deg	2.048
r_angle_other_deg	0.8
r_chiral_restr	0.101
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_bond_other_d	0.004
r_gen_planes_other	0.004
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	4824
Nucleic Acid Atoms
Solvent Atoms	303
Heterogen Atoms	86

Software

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