8UUB

Structure of hypothiocyanous acid reductase (Har) from Streptococcus pneumoniae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.152.4 M sodium malonate dibasic, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
3.3262.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.259α = 90
b = 122.259β = 90
c = 92.439γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.954Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.547.199.60.99915.226.6110989
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.530.754

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.547.1105305559099.560.159210.157970.18311RANDOM23.041
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]
0.080.08-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.164
r_dihedral_angle_4_deg17.129
r_dihedral_angle_3_deg12.723
r_dihedral_angle_1_deg6.509
r_long_range_B_refined6.029
r_scbond_it3.204
r_mcangle_it2.687
r_angle_refined_deg2.028
r_mcbond_it1.828
r_chiral_restr0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.164
r_dihedral_angle_4_deg17.129
r_dihedral_angle_3_deg12.723
r_dihedral_angle_1_deg6.509
r_long_range_B_refined6.029
r_scbond_it3.204
r_mcangle_it2.687
r_angle_refined_deg2.028
r_mcbond_it1.828
r_chiral_restr0.13
r_bond_refined_d0.014
r_gen_planes_refined0.014
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3343
Nucleic Acid Atoms
Solvent Atoms701
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
MrBUMPphasing
Cootmodel building
XDSdata reduction
Aimlessdata scaling