2HK6

Crystal Structure of B. subtilis ferrochelatase with Iron bound at the active site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DOZPDB ENTRY 1DOZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION828825% PEG 2000, 0.2 M MgCl2, 0.1 M Tris-HCl , pH 8.0, VAPOR DIFFUSION, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
2.0439.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.65α = 90
b = 49.98β = 90
c = 118.85γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2005-06-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-31.0605MAX III911-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.7201000.0270.05511.331884
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.71.8195.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1DOZ1.7119.642302883028815951000.178240.176090.21951RANDOM15.516
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]
0.57-1.030.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.791
r_dihedral_angle_4_deg17.977
r_dihedral_angle_3_deg12.07
r_dihedral_angle_1_deg4.926
r_scangle_it3.491
r_scbond_it2.262
r_angle_refined_deg1.347
r_mcangle_it1.295
r_mcbond_it0.818
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.791
r_dihedral_angle_4_deg17.977
r_dihedral_angle_3_deg12.07
r_dihedral_angle_1_deg4.926
r_scangle_it3.491
r_scbond_it2.262
r_angle_refined_deg1.347
r_mcangle_it1.295
r_mcbond_it0.818
r_nbtor_refined0.304
r_metal_ion_refined0.261
r_nbd_refined0.2
r_symmetry_vdw_refined0.182
r_xyhbond_nbd_refined0.152
r_symmetry_hbond_refined0.112
r_chiral_restr0.089
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2495
Nucleic Acid Atoms
Solvent Atoms368
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing