6IKK | pdb_00006ikk

Crystal structure of YfiB(L43P) in complex with YfiR

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ZHU	4ZHU, 4ZHW
experimental model	PDB	4ZHW	4ZHU, 4ZHW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	10%(w/v) PEG 6000, 0.1 M Bicine pH 9.0

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.798	α = 72.69
b = 58.413	β = 83.01
c = 70.324	γ = 89.33

Symmetry
Space Group	P 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	PIXEL	DECTRIS PILATUS 6M		2016-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.9791	SSRF	BL18U1

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	2.2	66.62	97.7	0.089	13	3.5		37342

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	2.2	2.27	95		0.462	3.6	3

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 (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	4ZHU, 4ZHW	2.19	66.62	35314	1999	96.91	0.18015	0.17884	0.19	0.20335	0.21	RANDOM	49.794

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]
0.22	0.42	-0.96	-0.08	0.38	-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.815
r_dihedral_angle_4_deg	15.834
r_dihedral_angle_3_deg	14.448
r_long_range_B_refined	7.98
r_long_range_B_other	7.926
r_dihedral_angle_1_deg	6.282
r_scangle_other	4.645
r_mcangle_it	3.595
r_mcangle_other	3.595
r_scbond_it	3.496
r_scbond_other	3.166
r_mcbond_it	2.435
r_mcbond_other	2.433
r_angle_refined_deg	1.543
r_angle_other_deg	0.986
r_chiral_restr	0.091
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
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	4217
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing