7Q4G

Structure of coproheme decarboxylase from Corynebacterium dipththeriae Y135A 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 DROP295.15PEG 3350, MgCl2, Sodium Phosphate
Crystal Properties
Matthews coefficientSolvent content
2.1943.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.117α = 90
b = 123.517β = 98.02
c = 78.3γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-FToroidal mirror2018-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.0723ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
11.8248.3197.650.19120.20740.07960.9955.736.665972227.41
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.821.88581.682.0790.94290.2214.6

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-VALUE6XUC1.8248.311.36100477210097.470.17390.17290.219435.54
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_d9.5689
f_angle_d1.047
f_chiral_restr0.1118
f_bond_d0.0153
f_plane_restr0.0127
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9334
Nucleic Acid Atoms
Solvent Atoms841
Heterogen Atoms252

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PDB-REDOrefinement
PHASERphasing
Cootmodel building