3HII

Crystal structure of human diamine oxidase in complex with the inhibitor pentamidine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HI7PDB ENTRY 3HI7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.1M bis-tris propane, 20%(w/v) PEG 3350, 0.2M sodium sulfate, pH 7.5, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5852.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.455α = 90
b = 94.69β = 90
c = 196.279γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOSMIC MIRRORS2008-11-05MSINGLE 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)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
12.14950950.1039.9033897518975129.96
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)
12.1492.2387.10.3362.72.48090

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONBY REFINEMENTTHROUGHOUTPDB ENTRY 3HI72.14925.848509385093455494.980.183590.181590.22093RANDOM21.017
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]
1.2-0.94-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.9
r_dihedral_angle_4_deg13.985
r_dihedral_angle_3_deg11.793
r_dihedral_angle_1_deg6.521
r_scangle_it1.932
r_angle_refined_deg1.199
r_scbond_it1.191
r_mcangle_it0.808
r_angle_other_deg0.784
r_mcbond_it0.431
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.9
r_dihedral_angle_4_deg13.985
r_dihedral_angle_3_deg11.793
r_dihedral_angle_1_deg6.521
r_scangle_it1.932
r_angle_refined_deg1.199
r_scbond_it1.191
r_mcangle_it0.808
r_angle_other_deg0.784
r_mcbond_it0.431
r_mcbond_other0.081
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11354
Nucleic Acid Atoms
Solvent Atoms916
Heterogen Atoms241

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing