2PIC

E. coli lytic transglycosylase MltA-D308A in apo-2 form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AE0PDB ENTRY 2AE0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.22980.25-0.35M NaCl, 10mM magnesium chloride, 100mM sodium acetate buffer, pH 4.2, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.2261.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.9α = 90
b = 80.9β = 90
c = 130.3γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.253093.90.06321.53.6228842288411
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)
12.252.33660.341584

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2AE02.25302270922709115594.590.2060.2060.2030.263RANDOM49.472
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]
1.250.621.25-1.87
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it10.065
r_scbond_it7.322
r_mcangle_it5.03
r_mcbond_it3.278
r_dihedral_angle_1_deg1.397
r_angle_refined_deg1.135
r_symmetry_vdw_refined0.194
r_nbd_refined0.19
r_xyhbond_nbd_refined0.113
r_chiral_restr0.105
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it10.065
r_scbond_it7.322
r_mcangle_it5.03
r_mcbond_it3.278
r_dihedral_angle_1_deg1.397
r_angle_refined_deg1.135
r_symmetry_vdw_refined0.194
r_nbd_refined0.19
r_xyhbond_nbd_refined0.113
r_chiral_restr0.105
r_symmetry_hbond_refined0.062
r_bond_refined_d0.005
r_gen_planes_refined0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2640
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ProDCdata collection
MOLREPphasing