8OIM

Crystal structure of the lipase SpL from Sphingomonas sp. HXN-200

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	RoseTTAFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	289	5 mg/ml SPL, Index screen condition 78 (0.2 M Ammonium acetate, 0.1 M BIS-TRIS, 25% PEG 3350)

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.812	α = 90
b = 88.966	β = 96.411
c = 65.627	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER2 X 16M		2021-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.033210	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	1.99	42.05	94.9	0.071	0.099	0.068	0.992	9.5	3.4		44854

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	1.99	2.05			0.281	0.392	0.273	0.925		3.4

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	1.994	42.048	44805	2309	94.571	0.167	0.1647	0.2017	30.462

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]
-1.029		0.507	1.902		-0.962

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.943
r_dihedral_angle_3_deg	15.415
r_lrange_it	9.53
r_lrange_other	9.493
r_scangle_it	8.644
r_scangle_other	8.643
r_dihedral_angle_2_deg	8.198
r_dihedral_angle_1_deg	6.966
r_scbond_it	6.051
r_scbond_other	6.05
r_mcangle_other	4.705
r_mcangle_it	4.704
r_mcbond_it	3.776
r_mcbond_other	3.76
r_angle_refined_deg	2.037
r_angle_other_deg	0.641
r_nbd_refined	0.214
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.184
r_symmetry_xyhbond_nbd_refined	0.162
r_nbd_other	0.138
r_chiral_restr	0.106
r_ncsr_local_group_1	0.088
r_symmetry_nbtor_other	0.085
r_symmetry_nbd_refined	0.057
r_symmetry_xyhbond_nbd_other	0.021
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4674
Nucleic Acid Atoms
Solvent Atoms	360
Heterogen Atoms

Software

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