7Q4F

Structure of coproheme decarboxylase from Corynebacterium dipththeriae W183Y mutant in complex with coproheme


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6XUC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP295.1520 %w/v PEG 3350 (Polymer), 0.1 M CBTP 6.4 pH (Buffer)
Crystal Properties
Matthews coefficientSolvent content
2.6653.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.809α = 90
b = 141.809β = 90
c = 124.863γ = 120
Symmetry
Space GroupP 3 1 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 2MKB mirror2021-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8731ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.1543.50996.950.37830.38830.9949.3719.977872
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.2274.2590.2230.64

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6XUC2.1543.51523.7570973213191.10.14160.13950.182244.05
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d10.2379
f_angle_d0.6021
f_chiral_restr0.0455
f_plane_restr0.0046
f_bond_d0.0037
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9370
Nucleic Acid Atoms
Solvent Atoms648
Heterogen Atoms269

Software

Software
Software NamePurpose
PDB-REDOrefinement
PHENIXrefinement
XDSdata reduction
EDNAdata collection
PHASERphasing