1IW0 | pdb_00001iw0

Crystal structure of a heme oxygenase (HmuO) from Corynebacterium diphtheriae complexed with heme in the ferric state

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.8	303	ammonium sulfate, NaI, MES, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 303K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.559	α = 90
b = 62.838	β = 100.86
c = 107.661	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	98	CCD	RIGAKU JUPITER 210	mirrors	2001-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45PX	0.9	SPring-8	BL45PX

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	1.3	99	85	0.034	18.08		261943	146822

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)
	1.3	1.34	58.6		0.297	0.87

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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		THROUGHOUT	1.4	12	111789	111789	12385	90.11	0.168	0.168	0.16541	0.17	0.19187	0.19	RANDOM	15.799

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]
0.01		0.3	0.47		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	13.124
r_scangle_it	3.897
r_dihedral_angle_1_deg	3.587
r_sphericity_free	2.594
r_scbond_it	2.464
r_sphericity_bonded	1.933
r_angle_refined_deg	1.736
r_mcangle_it	1.705
r_rigid_bond_restr	1.349
r_angle_other_deg	1.347
r_mcbond_it	1.006
r_nbtor_other	0.551
r_symmetry_vdw_other	0.252
r_nbd_refined	0.238
r_xyhbond_nbd_refined	0.189
r_nbd_other	0.187
r_symmetry_hbond_refined	0.178
r_symmetry_vdw_refined	0.152
r_xyhbond_nbd_other	0.136
r_chiral_restr	0.092
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_symmetry_hbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4996
Nucleic Acid Atoms
Solvent Atoms	657
Heterogen Atoms	185

Software

Software
Software Name	Purpose
Jupiter210	data collection
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
JUPITER210	data reduction