8B4N | pdb_00008b4n

X-ray structure of phycoerythrin from Porphyridium cruentum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3V58

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	PE crystals were grown by hanging drop vapor diffusion method (Russo Krauss et al., 2013) using a drop containing 10 mg/mL PE in 0.250 M ammonium sulphate, 25.0 mM potassium phosphate at pH 5.0, equilibrated with a reservoir containing 0.500 M ammonium sulphate, 50.0 mM potassium phosphate at pH 5.0.

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 186.59	α = 90
b = 186.59	β = 90
c = 59.19	γ = 120

Symmetry
Space Group	H 3

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		2022-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.00	ELETTRA	11.2C

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	1.597	46.648	99	0.101	0.107	0.035	0.997	12.9	9.2		100909

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	1.597	1.625	98.3		1.028	0.999	0.36	0.595	2.2	9

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	3V58	1.6	46.648	100412	4971	98.994	0.223	0.2217	0.23	0.2564	0.26	23.932

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]
-0.061	-0.031		-0.061		0.199

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.983
r_dihedral_angle_4_deg	14.893
r_dihedral_angle_3_deg	13.457
r_dihedral_angle_1_deg	5.821
r_lrange_it	4.18
r_lrange_other	4.143
r_scangle_it	3.373
r_scangle_other	3.368
r_mcangle_it	2.439
r_mcangle_other	2.439
r_scbond_it	2.387
r_scbond_other	2.377
r_mcbond_it	1.862
r_mcbond_other	1.861
r_angle_refined_deg	1.602
r_angle_other_deg	1.477
r_nbd_refined	0.284
r_xyhbond_nbd_other	0.238
r_symmetry_nbd_other	0.209
r_xyhbond_nbd_refined	0.18
r_nbd_other	0.174
r_nbtor_refined	0.166
r_symmetry_nbd_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.161
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5070
Nucleic Acid Atoms
Solvent Atoms	324
Heterogen Atoms	458

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing