6Y3D

X-ray structure of thermophilic C-phycocyanin from Galdiera phlegrea

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.10 M Hepes, 0.20 M magnesium chloride and 9.0 % (w/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.03	α = 90
b = 189.13	β = 90
c = 208.13	γ = 90

Symmetry
Space Group	P 2 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	DECTRIS PILATUS3 S 6M		2019-06-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	0.96	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	1.8	94.744	92.5	0.199	0.255	0.119	0.981	2.7	4.4		217082

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	79.6		1.8	0.061		3.6

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	3brp	1.8	94.744	216823	11108	98.661	0.223	0.2211	0.2682	30.779

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]
1.698			-1.668		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.066
r_dihedral_angle_4_deg	17.181
r_dihedral_angle_3_deg	15.401
r_lrange_it	6.244
r_lrange_other	6.169
r_dihedral_angle_1_deg	5.659
r_scangle_it	5.131
r_scangle_other	5.131
r_scbond_it	3.4
r_scbond_other	3.4
r_mcangle_other	3.303
r_mcangle_it	3.302
r_mcbond_it	2.384
r_mcbond_other	2.38
r_angle_refined_deg	1.598
r_angle_other_deg	1.413
r_nbd_refined	0.23
r_xyhbond_nbd_refined	0.198
r_symmetry_nbd_refined	0.193
r_symmetry_nbd_other	0.19
r_nbd_other	0.167
r_symmetry_xyhbond_nbd_refined	0.164
r_nbtor_refined	0.161
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.08
r_symmetry_xyhbond_nbd_other	0.028
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14874
Nucleic Acid Atoms
Solvent Atoms	1215
Heterogen Atoms	788

Software

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