8P7E

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8OIM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	5 mg/ml SPL, 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.97	α = 90
b = 88.552	β = 96.17
c = 65.761	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		2021-11-26	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	1.5	36.66	98.9	0.105	0.125	0.066	0.995	11.5	6.8		110029

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	1.5	1.52			0.573	0.682	0.364	0.874		6.4

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	1.5	36.66	109867	5447	99.008	0.139	0.1376	0.1577	15.039

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]
0.052		0.387	0.553		-0.673

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.77
r_dihedral_angle_3_deg	14.276
r_dihedral_angle_2_deg	7.677
r_lrange_it	6.311
r_dihedral_angle_1_deg	6.017
r_lrange_other	5.842
r_scangle_it	4.696
r_scangle_other	4.695
r_scbond_it	3.075
r_scbond_other	3.075
r_mcangle_it	2.366
r_mcangle_other	2.365
r_angle_refined_deg	1.738
r_mcbond_it	1.633
r_mcbond_other	1.607
r_angle_other_deg	0.586
r_symmetry_xyhbond_nbd_refined	0.31
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.208
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.184
r_nbd_other	0.15
r_symmetry_nbd_refined	0.107
r_chiral_restr	0.097
r_symmetry_nbtor_other	0.082
r_ncsr_local_group_1	0.073
r_symmetry_xyhbond_nbd_other	0.06
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
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	899
Heterogen Atoms	96

Software

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