4GOH

Structure of the substrate-free HmuO, HO from Corynebacterium diphtheriae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.5293PEG8000, Sodium Acetate, Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3247.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.489α = 90
b = 61.916β = 90
c = 63.086γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 3152004-10-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.85098.42134821006
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8697.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.8302100618909206598.260.178680.178680.174710.21615RANDOM20.97
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]
-1.12-0.31.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.499
r_dihedral_angle_3_deg14.874
r_dihedral_angle_4_deg13.696
r_dihedral_angle_1_deg5.544
r_scangle_it4.426
r_scbond_it2.796
r_mcangle_it1.97
r_angle_other_deg1.838
r_angle_refined_deg1.729
r_mcbond_it1.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.499
r_dihedral_angle_3_deg14.874
r_dihedral_angle_4_deg13.696
r_dihedral_angle_1_deg5.544
r_scangle_it4.426
r_scbond_it2.796
r_mcangle_it1.97
r_angle_other_deg1.838
r_angle_refined_deg1.729
r_mcbond_it1.091
r_symmetry_vdw_other0.356
r_mcbond_other0.292
r_symmetry_vdw_refined0.287
r_nbd_refined0.233
r_nbd_other0.2
r_metal_ion_refined0.2
r_nbtor_refined0.188
r_xyhbond_nbd_refined0.151
r_chiral_restr0.123
r_symmetry_hbond_refined0.123
r_nbtor_other0.096
r_bond_refined_d0.019
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
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 AtomsNumber
Protein Atoms1670
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms38

Software

Software
Software NamePurpose
ADSCdata collection
CNSrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing