4AW9

Crystal structure of active legumain in complex with YVAD-CMK


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1 M HEPES PH 7.5, 0.2 M LITHIUM SULFATE MONOHYDRATE, 25 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4849

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.14α = 90
b = 64.14β = 90
c = 78.95γ = 90
Symmetry
Space GroupP 42

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.1849.791000.1217.414.316856
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)
12.182.291000.495.814.2

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 DIFFRACTIONSIRASTHROUGHOUTNONE2.2481389381590.120.18170.180310.207RANDOM31.15
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]
-0.67-0.671.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.278
r_dihedral_angle_3_deg14.358
r_dihedral_angle_4_deg5.69
r_dihedral_angle_1_deg4.944
r_angle_refined_deg1.038
r_chiral_restr0.063
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.278
r_dihedral_angle_3_deg14.358
r_dihedral_angle_4_deg5.69
r_dihedral_angle_1_deg4.944
r_angle_refined_deg1.038
r_chiral_restr0.063
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2151
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling