6LU4 | pdb_00006lu4

Crystal structure of the substrate binding protein from Microbacterium hydrocarbonoxydans complexed with propylparaben

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6LU3

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
2.23	44.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.083	α = 90
b = 77.17	β = 90
c = 121.35	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 PILATUS3 S 6M		2018-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

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	2.8	50	98.8	0.152	0.974	35.4	3.2		12261

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	2.8	2.85	98.8		0.413	0.794	2.2	3.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6LU3	2.8	47.743	12231	618	98.852	0.209	0.2072	0.21	0.247	0.25	44.864

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]
-2.179			2.129		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.148
r_dihedral_angle_4_deg	19.653
r_dihedral_angle_3_deg	18.854
r_dihedral_angle_1_deg	10.668
r_lrange_it	4.87
r_lrange_other	4.87
r_scangle_it	3.171
r_scangle_other	3.17
r_mcangle_it	3.099
r_mcangle_other	3.099
r_angle_other_deg	2.424
r_mcbond_it	1.934
r_mcbond_other	1.934
r_scbond_it	1.887
r_scbond_other	1.886
r_angle_refined_deg	1.359
r_symmetry_nbd_other	0.219
r_nbd_other	0.208
r_symmetry_xyhbond_nbd_refined	0.197
r_nbd_refined	0.187
r_xyhbond_nbd_refined	0.16
r_nbtor_refined	0.156
r_symmetry_xyhbond_nbd_other	0.141
r_symmetry_nbd_refined	0.114
r_symmetry_nbtor_other	0.071
r_chiral_restr	0.055
r_bond_other_d	0.037
r_gen_planes_other	0.005
r_bond_refined_d	0.004
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3544
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	13

Software

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