3HIG | pdb_00003hig

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

X-RAY DIFFRACTION

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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
2.59	52.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.662	α = 90
b = 94.884	β = 90
c = 196.411	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	CCD	ADSC QUANTUM 210r		2009-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.95663	Australian Synchrotron	MX1

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	2.09	50	96.7	0.139	10.81	4.7	98904	98904			22.352

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	2.09	2.18	91.8		0.61	2.4	4.4	9282

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	2.09	47.46	98837	93778	5059	96.44	0.17052	0.1684	0.17	0.20983	0.21	RANDOM	16.579

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]
0.3			-0.37		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.986
r_dihedral_angle_4_deg	15.731
r_dihedral_angle_3_deg	12.368
r_dihedral_angle_1_deg	6.732
r_scangle_it	2.889
r_scbond_it	1.817
r_angle_refined_deg	1.389
r_mcangle_it	1.168
r_angle_other_deg	0.839
r_mcbond_it	0.629
r_mcbond_other	0.145
r_chiral_restr	0.084
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
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	11362
Nucleic Acid Atoms
Solvent Atoms	952
Heterogen Atoms	233

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