8OIM

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelRoseTTAFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52895 mg/ml SPL, Index screen condition 78 (0.2 M Ammonium acetate, 0.1 M BIS-TRIS, 25% PEG 3350)
Crystal Properties
Matthews coefficientSolvent content
2.4950.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.812α = 90
b = 88.966β = 96.411
c = 65.627γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2021-10-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.033210PETRA III, DESYP11

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9942.0594.90.0710.0990.0680.9929.53.444854
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)RedundancyNumber Unique Reflections (All)
11.992.050.2810.3920.2730.9253.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.99442.04844805230994.5710.1670.16470.201730.462
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]
-1.0290.5071.902-0.962
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.943
r_dihedral_angle_3_deg15.415
r_lrange_it9.53
r_lrange_other9.493
r_scangle_it8.644
r_scangle_other8.643
r_dihedral_angle_2_deg8.198
r_dihedral_angle_1_deg6.966
r_scbond_it6.051
r_scbond_other6.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.943
r_dihedral_angle_3_deg15.415
r_lrange_it9.53
r_lrange_other9.493
r_scangle_it8.644
r_scangle_other8.643
r_dihedral_angle_2_deg8.198
r_dihedral_angle_1_deg6.966
r_scbond_it6.051
r_scbond_other6.05
r_mcangle_other4.705
r_mcangle_it4.704
r_mcbond_it3.776
r_mcbond_other3.76
r_angle_refined_deg2.037
r_angle_other_deg0.641
r_nbd_refined0.214
r_symmetry_nbd_other0.198
r_nbtor_refined0.184
r_xyhbond_nbd_refined0.184
r_symmetry_xyhbond_nbd_refined0.162
r_nbd_other0.138
r_chiral_restr0.106
r_ncsr_local_group_10.088
r_symmetry_nbtor_other0.085
r_symmetry_nbd_refined0.057
r_symmetry_xyhbond_nbd_other0.021
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4674
Nucleic Acid Atoms
Solvent Atoms360
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing