6LU3 | pdb_00006lu3

Crystal structure of a substrate binding protein from Microbacterium hydrocarbonoxydans complexed with 4-hydroxybenzoate hydrazide

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) PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.296	α = 90
b = 77.561	β = 90
c = 121.711	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	95	PIXEL	DECTRIS EIGER X 4M		2018-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	1.1	Photon Factory	BL-1A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.2	50	98.9	0.203	0.993	13.4	5.5		25212

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	2.2	2.24	98.2		0.627	0.756	2.4	4.2

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	2.2	47.314	25168	1297	98.048	0.21	0.2086	0.2109	0.2297	0.2325	28.864

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]
-0.455			0.574		-0.119

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.967
r_dihedral_angle_4_deg	18.337
r_dihedral_angle_3_deg	15.707
r_dihedral_angle_1_deg	10.549
r_lrange_it	3.962
r_lrange_other	3.962
r_scangle_it	2.772
r_scangle_other	2.772
r_angle_other_deg	2.412
r_mcangle_it	2.369
r_mcangle_other	2.368
r_scbond_it	1.699
r_scbond_other	1.698
r_mcbond_it	1.471
r_mcbond_other	1.471
r_angle_refined_deg	1.464
r_nbd_other	0.338
r_symmetry_nbd_refined	0.323
r_symmetry_nbd_other	0.208
r_nbd_refined	0.186
r_nbtor_refined	0.154
r_xyhbond_nbd_refined	0.14
r_symmetry_xyhbond_nbd_refined	0.105
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.071
r_chiral_restr_other	0.056
r_bond_other_d	0.037
r_symmetry_xyhbond_nbd_other	0.014
r_bond_refined_d	0.006
r_gen_planes_other	0.006
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3537
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CRANK2	phasing