5AVD

The 0.86 angstrom structure of elastase crystallized in high-strength agarose hydrogel


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GVK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH52930.1 M Na acetate (pH 5.0), 0.03 M (NH4)2SO4
Crystal Properties
Matthews coefficientSolvent content
2.0941.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.992α = 90
b = 58.21β = 90
c = 74.425γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102009-01-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A0.90000Photon FactoryAR-NW12A

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
10.865094.70.08810.310.8174535
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)
10.860.8777.10.6122.25.5

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 REPLACEMENTTHROUGHOUT1GVK0.8645.85165717877594.670.12860.127990.13988RANDOM10.282
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]
-0.01-0.030.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.913
r_dihedral_angle_4_deg20.86
r_sphericity_free16.93
r_dihedral_angle_3_deg12.238
r_rigid_bond_restr9.573
r_dihedral_angle_1_deg6.505
r_sphericity_bonded5.708
r_long_range_B_refined2.64
r_long_range_B_other2.401
r_angle_refined_deg2.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.913
r_dihedral_angle_4_deg20.86
r_sphericity_free16.93
r_dihedral_angle_3_deg12.238
r_rigid_bond_restr9.573
r_dihedral_angle_1_deg6.505
r_sphericity_bonded5.708
r_long_range_B_refined2.64
r_long_range_B_other2.401
r_angle_refined_deg2.38
r_scangle_other2.299
r_scbond_it2.282
r_scbond_other2.231
r_mcangle_it1.88
r_mcangle_other1.88
r_mcbond_other1.393
r_mcbond_it1.391
r_angle_other_deg1.345
r_chiral_restr0.144
r_bond_refined_d0.047
r_gen_planes_refined0.013
r_gen_planes_other0.005
r_bond_other_d0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1822
Nucleic Acid Atoms
Solvent Atoms274
Heterogen Atoms10

Software

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