3A6Z

Crystal structure of Pseudomonas sp. MIS38 lipase (PML) in the open conformation following dialysis against Ca-free buffer


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 acetate, 30% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.0259.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.382α = 90
b = 104.382β = 90
c = 495.175γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker DIP-6040mirrors2009-02-27MSINGLE 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
12.155099.30.1360.10913.766.987709
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.152.2399.20.4373.15.68579

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 2ZVD2.1548.1183266439799.450.184310.182440.21965RANDOM21.34
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]
0.010.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.304
r_dihedral_angle_4_deg22.138
r_dihedral_angle_3_deg15.402
r_dihedral_angle_1_deg7.276
r_scangle_it3.61
r_scbond_it2.542
r_angle_refined_deg1.724
r_mcangle_it1.573
r_mcbond_it0.977
r_symmetry_hbond_refined0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.304
r_dihedral_angle_4_deg22.138
r_dihedral_angle_3_deg15.402
r_dihedral_angle_1_deg7.276
r_scangle_it3.61
r_scbond_it2.542
r_angle_refined_deg1.724
r_mcangle_it1.573
r_mcbond_it0.977
r_symmetry_hbond_refined0.51
r_nbtor_refined0.306
r_symmetry_vdw_refined0.276
r_nbd_refined0.22
r_xyhbond_nbd_refined0.172
r_chiral_restr0.122
r_metal_ion_refined0.099
r_bond_refined_d0.019
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9078
Nucleic Acid Atoms
Solvent Atoms631
Heterogen Atoms17

Software

Software
Software NamePurpose
BL44XUdata collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling