5M47

Crystal structure of DapF from Corynebacterium glutamicum in complex with D,L-diaminopimelate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5H2Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9293Sodium citrate, CHES
Crystal Properties
Matthews coefficientSolvent content
5.376.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 155.695α = 90
b = 155.695β = 90
c = 155.695γ = 90
Symmetry
Space GroupP 43 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702015-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.97934PAL/PLS7A (6B, 6C1)

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
12.59110.197.40.1150.34421.11219071
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)
12.62.6493.40.34444.5

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 REPLACEMENTTHROUGHOUT5H2Y2.59110.091907197697.490.19320.19140.2292RANDOM34.446
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
r_dihedral_angle_2_deg40.374
r_dihedral_angle_4_deg17.697
r_dihedral_angle_3_deg17.16
r_dihedral_angle_1_deg8.478
r_mcangle_it4.387
r_mcbond_it2.71
r_mcbond_other2.534
r_angle_refined_deg2.103
r_angle_other_deg1.122
r_chiral_restr0.116
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.374
r_dihedral_angle_4_deg17.697
r_dihedral_angle_3_deg17.16
r_dihedral_angle_1_deg8.478
r_mcangle_it4.387
r_mcbond_it2.71
r_mcbond_other2.534
r_angle_refined_deg2.103
r_angle_other_deg1.122
r_chiral_restr0.116
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2073
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
HKLdata reduction