3K5T

Crystal structure of human diamine oxidase in space group C2221


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C10PDB entry 2c10

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.12980.1 M MES (pH 6.1), 12% w/v PEG 20,000, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4549.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.771α = 90
b = 96.954β = 90
c = 178.06γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOSMIC MIRRORS2007-01-11MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 210r2008-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418
2SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.957Australian SynchrotronMX1

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
1,22.106178.0695.20.1110.11115.77.44520025.3
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)
1,22.12.2196.20.2990.2992.536562

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 REPLACEMENTTHROUGHOUTPDB entry 2c102.1189.094519945199228894.550.2390.2390.2360.29RANDOM26.043
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]
-1.95-1.743.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.806
r_dihedral_angle_4_deg15.268
r_dihedral_angle_3_deg13.578
r_dihedral_angle_1_deg6.739
r_scangle_it1.792
r_angle_refined_deg1.224
r_scbond_it1.136
r_angle_other_deg0.82
r_mcangle_it0.777
r_mcbond_it0.431
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.806
r_dihedral_angle_4_deg15.268
r_dihedral_angle_3_deg13.578
r_dihedral_angle_1_deg6.739
r_scangle_it1.792
r_angle_refined_deg1.224
r_scbond_it1.136
r_angle_other_deg0.82
r_mcangle_it0.777
r_mcbond_it0.431
r_mcbond_other0.082
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5587
Nucleic Acid Atoms
Solvent Atoms299
Heterogen Atoms79

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing