1YS1

Burkholderia cepacia lipase complexed with hexylphosphonic acid (R)-2-methyl-3-phenylpropyl ester


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LIPPDB entry 3LIP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529350 mM imidazole, 30% n-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2445.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.848α = 90
b = 46.185β = 121.27
c = 84.626γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42000-05-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X8CNSLSX8C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
11.144.4289.20.04120.994.68105990115.41

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3LIP1.144.42100662532689.170.149870.149430.15841RANDOM7.213
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]
0.14-0.120.18-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.716
r_scangle_it2.107
r_scbond_it1.355
r_angle_refined_deg1.287
r_mcangle_it0.943
r_angle_other_deg0.773
r_mcbond_it0.532
r_nbd_other0.249
r_nbd_refined0.239
r_symmetry_vdw_other0.217
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.716
r_scangle_it2.107
r_scbond_it1.355
r_angle_refined_deg1.287
r_mcangle_it0.943
r_angle_other_deg0.773
r_mcbond_it0.532
r_nbd_other0.249
r_nbd_refined0.239
r_symmetry_vdw_other0.217
r_metal_ion_refined0.087
r_nbtor_other0.083
r_chiral_restr0.075
r_symmetry_vdw_refined0.074
r_xyhbond_nbd_refined0.068
r_symmetry_hbond_refined0.054
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.004
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2331
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing