3I8R | pdb_00003i8r

Crystal structure of the heme oxygenase from Corynebacterium diphtheriae (HmuO) in complex with heme binding ditiothreitol (DTT)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IW0	PDB ENTRY 1IW0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.1	303	2.2M (NH4)2SO4, 50mM MES (pH6.1), 0.1% Dioxane, 0.25M Sodium Iodide with 50mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 303K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.117	α = 90
b = 62.563	β = 100.67
c = 108.002	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	CCD	ADSC QUANTUM 210		2004-05-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.5	50	98	0.05	45.5	7	113340	111073		1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.5	1.55	90.1		0.378	2.62	6.3	10120

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1IW0	1.5	30	99940	11109	98.03	0.19698	0.19399	0.2	0.22351	0.23	RANDOM	25.139

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]
-0.38		0.37	1.38		-0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.72
r_dihedral_angle_4_deg	19.162
r_dihedral_angle_3_deg	14.875
r_scangle_it	5.639
r_dihedral_angle_1_deg	5.169
r_scbond_it	3.732
r_angle_refined_deg	2.519
r_mcangle_it	2.351
r_mcbond_it	1.494
r_chiral_restr	0.181
r_bond_refined_d	0.03
r_gen_planes_refined	0.015
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4957
Nucleic Acid Atoms
Solvent Atoms	484
Heterogen Atoms	198

Software

Software
Software Name	Purpose
CNS	refinement
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing