2IIZ

Crystal structure of putative melanin biosynthesis protein TyrA with bound heme (NP_716371.1) from Shewanella Oneidensis at 2.30 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HAG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82870.1M Tris, 5% isopropyl alcohol, 20% (w/v) polyethylene glycol 4000, additive - 1mM hemin, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties
Matthews coefficientSolvent content
3.5865.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.837α = 90
b = 94.837β = 90
c = 116.666γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Flat mirror (vertical focusing)2006-07-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-1SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.319.999.70.14211.726.952421038.592
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.451000.55234094

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 REPLACEMENTTHROUGHOUT2HAG2.319.824207126999.880.2080.2050.266RANDOM33.304
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]
-1.39-1.392.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.049
r_dihedral_angle_4_deg16.274
r_dihedral_angle_3_deg13.869
r_dihedral_angle_1_deg6.456
r_scangle_it5.78
r_scbond_it4.387
r_mcangle_it2.281
r_angle_refined_deg1.357
r_mcbond_it1.33
r_angle_other_deg0.763
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.049
r_dihedral_angle_4_deg16.274
r_dihedral_angle_3_deg13.869
r_dihedral_angle_1_deg6.456
r_scangle_it5.78
r_scbond_it4.387
r_mcangle_it2.281
r_angle_refined_deg1.357
r_mcbond_it1.33
r_angle_other_deg0.763
r_mcbond_other0.329
r_symmetry_hbond_refined0.292
r_symmetry_vdw_refined0.255
r_symmetry_vdw_other0.24
r_nbd_refined0.203
r_nbd_other0.19
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.134
r_nbtor_other0.087
r_chiral_restr0.076
r_bond_refined_d0.013
r_bond_other_d0.002
r_gen_planes_refined0.001
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2441
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms56

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
MolProbitymodel building
PDB_EXTRACTdata extraction
XDSdata reduction