4EP6 | pdb_00004ep6

Crystal structure of the XplA heme domain in complex with imidazole and PEG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WIVPDB ENTRY 2WIV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.527750 mM magnesium chloride, 0.1 M imidazole/MES, pH 6.5, 30% PEG550 MME, PEG20000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
4.0169.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.12α = 90
b = 136.12β = 90
c = 75.13γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I041DiamondI04

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
12.343.041002898328983

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2WIV2.343.04289832898315341000.202970.202970.200890.20.241790.24RANDOM43.021
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]
-3.45-3.456.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.69
r_dihedral_angle_4_deg16.789
r_dihedral_angle_3_deg15.192
r_dihedral_angle_1_deg6.827
r_scangle_it4.588
r_scbond_it2.884
r_angle_refined_deg1.885
r_mcangle_it1.716
r_angle_other_deg1.077
r_mcbond_it0.914
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.69
r_dihedral_angle_4_deg16.789
r_dihedral_angle_3_deg15.192
r_dihedral_angle_1_deg6.827
r_scangle_it4.588
r_scbond_it2.884
r_angle_refined_deg1.885
r_mcangle_it1.716
r_angle_other_deg1.077
r_mcbond_it0.914
r_mcbond_other0.213
r_chiral_restr0.11
r_bond_refined_d0.023
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3056
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms64

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling