3KVE

Structure of native L-amino acid oxidase from Vipera ammodytes ammodytes: stabilization of the quaternary structure by divalent ions and structural changes in the dynamic active site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F8RPDB entry 1F8R

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.3247.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 196.978α = 90
b = 95.839β = 92.53
c = 108.442γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2008-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8EMBL/DESY, HAMBURGX13

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
12.5727.497.10.17210.67.163563627171119.3
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)
2.572.6674.70.4483.94853

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 REPLACEMENTTHROUGHOUTPDB entry 1F8R2.5727.460346321298.040.195370.191050.27609RANDOM19.805
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]
10.11-0.74-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.41
r_dihedral_angle_4_deg20.408
r_dihedral_angle_3_deg20.38
r_dihedral_angle_1_deg7.474
r_scangle_it2.395
r_angle_refined_deg1.523
r_scbond_it1.467
r_mcangle_it1.018
r_mcbond_it0.573
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.41
r_dihedral_angle_4_deg20.408
r_dihedral_angle_3_deg20.38
r_dihedral_angle_1_deg7.474
r_scangle_it2.395
r_angle_refined_deg1.523
r_scbond_it1.467
r_mcangle_it1.018
r_mcbond_it0.573
r_nbtor_refined0.319
r_nbd_refined0.227
r_xyhbond_nbd_refined0.19
r_symmetry_vdw_refined0.173
r_metal_ion_refined0.164
r_symmetry_hbond_refined0.138
r_chiral_restr0.111
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15456
Nucleic Acid Atoms
Solvent Atoms554
Heterogen Atoms272

Software

Software
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling