3MOO

Crystal structure of the HmuO, heme oxygenase from Corynebacterium diphtheriae, in complex with azide-bound verdoheme


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IW0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.430350mM MES (pH 5.4), 2.4M ammonium sulfate, 0.27M sodium bromide, 0.1 % (v/v) dioxane, VAPOR DIFFUSION, temperature 303K
Crystal Properties
Matthews coefficientSolvent content
2.141.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.609α = 90
b = 63.649β = 130.34
c = 78.52γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702008-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1.0Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.75096.20.05623.64.3637613
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.7282.80.2892.84

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1IW01.715035684415995.770.181880.178390.21283RANDOM
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]
-0.460.02-1.291.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.035
r_dihedral_angle_3_deg15.023
r_dihedral_angle_4_deg14.425
r_dihedral_angle_1_deg4.843
r_scangle_it3.526
r_angle_refined_deg2.469
r_scbond_it1.946
r_mcangle_it1.384
r_mcbond_it0.815
r_chiral_restr0.335
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.035
r_dihedral_angle_3_deg15.023
r_dihedral_angle_4_deg14.425
r_dihedral_angle_1_deg4.843
r_scangle_it3.526
r_angle_refined_deg2.469
r_scbond_it1.946
r_mcangle_it1.384
r_mcbond_it0.815
r_chiral_restr0.335
r_nbtor_refined0.301
r_symmetry_vdw_refined0.22
r_nbd_refined0.206
r_symmetry_hbond_refined0.183
r_xyhbond_nbd_refined0.149
r_metal_ion_refined0.104
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
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 AtomsNumber
Protein Atoms3312
Nucleic Acid Atoms
Solvent Atoms310
Heterogen Atoms188

Software

Software
Software NamePurpose
REFMACrefinement