8P8F

Crystal structure of the lipase SpL from Sphingomonas sp. HXN-200 in complex with N-benzyl-picolinamide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	5 mg/ml SPL, 0.02 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 22% w/v Poly(acrylic acid sodium salt) 5,100

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.833	α = 90
b = 60.833	β = 90
c = 217.692	γ = 90

Symmetry
Space Group	P 43

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 EIGER2 X 16M		2021-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.033190	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.8	46.62	100	0.142	0.154	0.06	0.996	11.3	12.6		72849

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	1.8	1.84			0.743	0.817	0.336	0.835		11.7

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.8	46.618	72765	3612	99.977	0.191	0.1886	0.2277	24.376

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]
-0.177			-0.177		0.354

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.899
r_dihedral_angle_3_deg	15.082
r_dihedral_angle_2_deg	7.647
r_lrange_it	6.721
r_lrange_other	6.619
r_dihedral_angle_1_deg	6.422
r_scangle_it	6.06
r_scangle_other	6.059
r_scbond_it	4.318
r_scbond_other	4.317
r_mcangle_it	3.626
r_mcangle_other	3.625
r_mcbond_it	2.976
r_mcbond_other	2.973
r_angle_refined_deg	1.84
r_angle_other_deg	1.037
r_symmetry_nbd_refined	0.581
r_nbd_other	0.242
r_nbd_refined	0.21
r_symmetry_nbd_other	0.21
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.147
r_symmetry_xyhbond_nbd_refined	0.139
r_chiral_restr	0.105
r_symmetry_nbtor_other	0.088
r_ncsr_local_group_1	0.065
r_gen_planes_other	0.021
r_bond_refined_d	0.014
r_gen_planes_refined	0.013
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4674
Nucleic Acid Atoms
Solvent Atoms	550
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
XDS	data reduction