6LU2 | pdb_00006lu2

Crystal structure of a substrate binding protein from Microbacterium hydrocarbonoxydans

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2 M sodium acetate 0.1 M sodium cacodylate, pH 7.5 30% (w/v) PEG8000

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.263	α = 90
b = 78.443	β = 90
c = 123.368	γ = 90

Symmetry
Space Group	P 21 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	CCD	RAYONIX MX225HE		2017-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	0.9785	SPring-8	BL38B1

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	1.75	50	99.3	0.092	50.6	13.2		48691

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	1.75	1.78	95.7		1.1	2.8	11.5

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.75	39.551	48619	2397	99.133	0.195	0.1941	0.2033	0.2064	0.216	25.381

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]
0.104			0.409		-0.513

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.45
r_dihedral_angle_4_deg	15.541
r_dihedral_angle_3_deg	12.983
r_dihedral_angle_1_deg	10.518
r_lrange_it	4.535
r_lrange_other	4.498
r_scangle_it	3.528
r_scangle_other	3.528
r_mcangle_it	2.454
r_mcangle_other	2.454
r_angle_other_deg	2.394
r_scbond_it	2.332
r_scbond_other	2.331
r_mcbond_it	1.657
r_mcbond_other	1.657
r_angle_refined_deg	1.465
r_symmetry_xyhbond_nbd_refined	0.213
r_symmetry_nbd_other	0.212
r_nbd_refined	0.198
r_nbd_other	0.174
r_nbtor_refined	0.159
r_xyhbond_nbd_refined	0.14
r_symmetry_nbd_refined	0.122
r_symmetry_xyhbond_nbd_other	0.077
r_symmetry_nbtor_other	0.069
r_chiral_restr	0.062
r_bond_other_d	0.037
r_gen_planes_other	0.009
r_bond_refined_d	0.008
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3546
Nucleic Acid Atoms
Solvent Atoms	347
Heterogen Atoms

Software

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