5ZUN

Crystal structure of human monoacylglycerol lipase in complex with compound 3l


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PE6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62930.1M Bis-Tris, 10% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.7355.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.149α = 90
b = 127.224β = 90
c = 60.25γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152014-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21ALS5.0.2

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
11.3550980.07422.66.978596
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)
11.351.3777.30.8521.54.3

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 REPLACEMENTTHROUGHOUT3PE61.354074657391697.830.147580.146930.16008RANDOM14.803
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]
1.38-0.69-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.758
r_dihedral_angle_4_deg18.116
r_dihedral_angle_3_deg13.097
r_dihedral_angle_1_deg5.832
r_long_range_B_refined4.353
r_long_range_B_other4.001
r_scangle_other2.007
r_angle_refined_deg1.603
r_mcangle_other1.428
r_mcangle_it1.424
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.758
r_dihedral_angle_4_deg18.116
r_dihedral_angle_3_deg13.097
r_dihedral_angle_1_deg5.832
r_long_range_B_refined4.353
r_long_range_B_other4.001
r_scangle_other2.007
r_angle_refined_deg1.603
r_mcangle_other1.428
r_mcangle_it1.424
r_scbond_it1.284
r_scbond_other1.282
r_mcbond_it0.834
r_mcbond_other0.833
r_angle_other_deg0.55
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2238
Nucleic Acid Atoms
Solvent Atoms297
Heterogen Atoms78

Software

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