2ZVD

Crystal structure of Pseudomonas sp. MIS38 lipase in an open conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Z8XPDB ENTRY 2Z8X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52770.2M ammonium acetate, 0.1M Tris-HCl, pH8.5, 30% isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Crystal Properties
Matthews coefficientSolvent content
3.0659.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.781α = 90
b = 104.781β = 90
c = 497.926γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker DIP-6040mirrors2008-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU1.0SPring-8BL44XU

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
12.1401000.1030.07727.710.917122495813
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)
2.12.181000.4060.4016.3119353

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 2Z8X2.154084781447399.990.1720.170010.20979RANDOM22.724
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]
-0.01-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.611
r_dihedral_angle_4_deg20.081
r_dihedral_angle_3_deg15.097
r_dihedral_angle_1_deg7.287
r_scangle_it3.883
r_scbond_it2.538
r_angle_refined_deg1.585
r_mcangle_it1.555
r_mcbond_it0.906
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.611
r_dihedral_angle_4_deg20.081
r_dihedral_angle_3_deg15.097
r_dihedral_angle_1_deg7.287
r_scangle_it3.883
r_scbond_it2.538
r_angle_refined_deg1.585
r_mcangle_it1.555
r_mcbond_it0.906
r_nbtor_refined0.305
r_symmetry_hbond_refined0.221
r_nbd_refined0.217
r_symmetry_vdw_refined0.201
r_xyhbond_nbd_refined0.164
r_chiral_restr0.115
r_metal_ion_refined0.11
r_bond_refined_d0.017
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9037
Nucleic Acid Atoms
Solvent Atoms1228
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
SPringdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing