5NPL | pdb_00005npl

Crystal structure of hexameric CBS-CP12 protein from bloom-forming cyanobacteria, Yb-derivative at 2.8 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	292	300 MM NA ACETATE, 20% PEG2000 MME, REMARK 280 100 MM HEPES BUFFER, PH 8.0; before data collection crystals were soaked for 30 min in a solution containing 25% PEG2000MME, 0.2 M sodium acetate, 0.1 M HEPES, pH 8.0 and 0.1 M Yb-HPDO3A

Crystal Properties
Matthews coefficient	Solvent content
2.13	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.89	α = 90
b = 120.734	β = 90
c = 117.548	γ = 90

Symmetry
Space Group	C 2 2 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	mirrors	2015-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	1.385	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.79	66	97.8	0.095	14.5	6.5		13464			51.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.79	2.87	61.2		0.63	1.77	2.7

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	SAD	THROUGHOUT	2.79	10	13151	677	95.52	0.18764	0.18593	0.2	0.21948	0.22	RANDOM	53.449

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]
5.23			2.17		-7.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.83
r_dihedral_angle_3_deg	17.404
r_dihedral_angle_4_deg	17.364
r_long_range_B_refined	6.247
r_long_range_B_other	6.245
r_dihedral_angle_1_deg	5.595
r_scangle_other	3.868
r_mcangle_it	3.662
r_mcangle_other	3.661
r_scbond_it	2.258
r_scbond_other	2.257
r_mcbond_it	2.139
r_mcbond_other	2.139
r_angle_refined_deg	1.779
r_angle_other_deg	1.027
r_chiral_restr	0.122
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
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	4120
Nucleic Acid Atoms
Solvent Atoms	51
Heterogen Atoms	73

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
CRANK2	phasing