2Z8Z

Crystal structure of a platinum-bound S445C mutant of Pseudomonas sp. MIS38 lipase


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP627720% PEG 20000, 0.1M MES, 0.2M calcium acetate, 5mM zinc acetate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.8256.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.879α = 90
b = 84.404β = 96.5
c = 87.012γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 210mirror2007-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.071784SPring-8BL38B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.8500.0747.265946634353.4

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 2Z8X1.832.1260247317899.280.175120.173530.20493RANDOM21.877
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.107
r_dihedral_angle_4_deg19.323
r_dihedral_angle_3_deg12.777
r_dihedral_angle_1_deg8.353
r_scangle_it3.952
r_scbond_it2.715
r_angle_refined_deg1.771
r_mcangle_it1.702
r_mcbond_it1.149
r_angle_other_deg1.047
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.107
r_dihedral_angle_4_deg19.323
r_dihedral_angle_3_deg12.777
r_dihedral_angle_1_deg8.353
r_scangle_it3.952
r_scbond_it2.715
r_angle_refined_deg1.771
r_mcangle_it1.702
r_mcbond_it1.149
r_angle_other_deg1.047
r_symmetry_metal_ion_refined0.793
r_mcbond_other0.346
r_nbd_refined0.233
r_symmetry_vdw_other0.196
r_nbd_other0.19
r_nbtor_refined0.183
r_chiral_restr0.173
r_symmetry_vdw_refined0.173
r_symmetry_hbond_refined0.164
r_xyhbond_nbd_refined0.149
r_metal_ion_refined0.11
r_nbtor_other0.087
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4553
Nucleic Acid Atoms
Solvent Atoms495
Heterogen Atoms14

Software

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