3A70

Crystal structure of Pseudomonas sp. MIS38 lipase in complex with diethyl phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZVDPDB ENTRY 2ZVD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52770.1M Tris-HCl, pH8.5, 0.2M ammonium acetaet, 30% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.0259.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.297α = 90
b = 104.297β = 90
c = 496.182γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210mirrors2009-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.0SPring-8BL38B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.155099.10.1240.11213.55.288120
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.152.231000.3780.3763.444.98629

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 2ZVD2.1531.9183034439399.210.172730.170120.22209RANDOM21.854
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.876
r_dihedral_angle_4_deg21.84
r_dihedral_angle_3_deg14.384
r_dihedral_angle_1_deg7.341
r_scangle_it3.667
r_scbond_it2.464
r_angle_refined_deg1.878
r_mcangle_it1.489
r_mcbond_it0.879
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.876
r_dihedral_angle_4_deg21.84
r_dihedral_angle_3_deg14.384
r_dihedral_angle_1_deg7.341
r_scangle_it3.667
r_scbond_it2.464
r_angle_refined_deg1.878
r_mcangle_it1.489
r_mcbond_it0.879
r_nbtor_refined0.304
r_symmetry_vdw_refined0.216
r_nbd_refined0.215
r_xyhbond_nbd_refined0.155
r_symmetry_hbond_refined0.145
r_chiral_restr0.116
r_metal_ion_refined0.106
r_bond_refined_d0.021
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9037
Nucleic Acid Atoms
Solvent Atoms1121
Heterogen Atoms66

Software

Software
Software NamePurpose
BL38B1data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling