4GLB

Structure of p-nitrobenzaldehyde inhibited lipase from Thermomyces lanuginosa at 2.69 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4EA6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.1M HEPES, O.1M Nacl, 1.6M Ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.8768.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.911α = 90
b = 139.911β = 90
c = 80.448γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHMirror2012-05-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

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
12.6950990.074232354648.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.692.74900.2733.748050

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4EA62.6950235461286990.16350.16350.16130.20543RANDOM36.973
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]
18.2918.29-36.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.54
r_dihedral_angle_4_deg21.478
r_dihedral_angle_3_deg16.232
r_dihedral_angle_1_deg5.856
r_scangle_it1.428
r_angle_refined_deg1.078
r_scbond_it0.84
r_mcangle_it0.821
r_mcbond_it0.444
r_chiral_restr0.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.54
r_dihedral_angle_4_deg21.478
r_dihedral_angle_3_deg16.232
r_dihedral_angle_1_deg5.856
r_scangle_it1.428
r_angle_refined_deg1.078
r_scbond_it0.84
r_mcangle_it0.821
r_mcbond_it0.444
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4142
Nucleic Acid Atoms
Solvent Atoms105
Heterogen Atoms34

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling