3HII | pdb_00003hii

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

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HI7	PDB ENTRY 3HI7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	0.1M bis-tris propane, 20%(w/v) PEG 3350, 0.2M sodium sulfate, pH 7.5, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.24

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	OSMIC MIRRORS	2008-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.149	50	95	0.103	9.903	3	89751	89751			29.96

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.149	2.23	87.1		0.336	2.7	2.4	8090

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	BY REFINEMENT	THROUGHOUT	PDB ENTRY 3HI7	2.149	25.84	85093	85093	4554	94.98	0.18359	0.18159	0.18	0.22093	0.22	RANDOM	21.017

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
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.9
r_dihedral_angle_4_deg	13.985
r_dihedral_angle_3_deg	11.793
r_dihedral_angle_1_deg	6.521
r_scangle_it	1.932
r_angle_refined_deg	1.199
r_scbond_it	1.191
r_mcangle_it	0.808
r_angle_other_deg	0.784
r_mcbond_it	0.431
r_mcbond_other	0.081
r_chiral_restr	0.07
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	11354
Nucleic Acid Atoms
Solvent Atoms	916
Heterogen Atoms	241

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing