2HB6

Structure of Caenorhabditis elegans leucine aminopeptidase (LAP1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EWB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6293100 MM MES, 2 M AMMONIUM SULFATE, PH 6.00, 5% GLYCEROL, 200 MM SODIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
358.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.82α = 90
b = 131.82β = 90
c = 125.573γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVMIRRORS2006-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
125099.90.0580.0935.712.48335983359
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)
122.0799.70.4230.4671.911.78253

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 REPLACEMENTTHROUGHOUT2EWB2208079080783249299.930.15230.148450.14740.18279RANDOM26.818
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]
-0.15-0.07-0.150.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.13
r_dihedral_angle_4_deg19.817
r_dihedral_angle_3_deg14.67
r_scangle_it7.393
r_dihedral_angle_1_deg7.314
r_scbond_it5.476
r_mcangle_it3.809
r_mcbond_it2.866
r_angle_refined_deg1.248
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.13
r_dihedral_angle_4_deg19.817
r_dihedral_angle_3_deg14.67
r_scangle_it7.393
r_dihedral_angle_1_deg7.314
r_scbond_it5.476
r_mcangle_it3.809
r_mcbond_it2.866
r_angle_refined_deg1.248
r_nbtor_refined0.302
r_metal_ion_refined0.274
r_symmetry_hbond_refined0.245
r_chiral_restr0.218
r_xyhbond_nbd_refined0.185
r_nbd_refined0.183
r_symmetry_vdw_refined0.171
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7330
Nucleic Acid Atoms
Solvent Atoms951
Heterogen Atoms108

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement