5ZYO | pdb_00005zyo

Crystal Structure of domain-swapped Circular-Permuted YbeA (CP74) from Escherichia coli

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293.15	25% PEG 8000, 0.1M PIPES
2	VAPOR DIFFUSION, SITTING DROP	7	293.15	25% PEG 8000, 0.1M PIPES

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.79
2.36	47.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.458	α = 90
b = 88.053	β = 101.47
c = 81.184	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX300HE		2018-03-12	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	ADSC QUANTUM 315r		2017-12-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL15A1	1.00928	NSRRC	BL15A1
2	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.0000	NSRRC	BL13B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.75	30	99.5	0.033	0.039	0.02	34.82	3.7		65452

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	1.75	1.81	98.1		0.439	0.525	0.285	0.824	2.13	3.1

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	1.75	29.52	62103	3326	99.25	0.1706	0.16933	0.17	0.19466	0.19	RANDOM	43.475

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]
0.74		-0.3	-0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.805
r_dihedral_angle_3_deg	16.909
r_dihedral_angle_4_deg	16.718
r_long_range_B_refined	8.586
r_scbond_it	7.084
r_mcangle_it	6.658
r_dihedral_angle_1_deg	5.712
r_mcbond_it	5.478
r_rigid_bond_restr	4.087
r_angle_refined_deg	1.381
r_chiral_restr	0.102
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4704
Nucleic Acid Atoms
Solvent Atoms	351
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data scaling
HKL-2000	data reduction
PHENIX	phasing