3D2Z

Complex of the N-acetylmuramyl-L-alanine amidase AmiD from E.coli with the product L-Ala-D-gamma-Glu-L-Lys


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP42931M LICL, 10 % PEG 6K, 0.1M ZNCL2, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.5465.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.16α = 90
b = 89.16β = 90
c = 183.64γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2007-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
12.847.91000.26314.620.411312
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)
12.82.951000.6984.9211592

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2BGX2.847.91070655199.960.205260.202110.26469RANDOM18.079
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]
0.310.160.31-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.415
r_dihedral_angle_3_deg16.723
r_dihedral_angle_4_deg16.008
r_dihedral_angle_1_deg6.368
r_mcangle_it1.537
r_angle_refined_deg1.356
r_scangle_it1.069
r_mcbond_it0.894
r_scbond_it0.647
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.415
r_dihedral_angle_3_deg16.723
r_dihedral_angle_4_deg16.008
r_dihedral_angle_1_deg6.368
r_mcangle_it1.537
r_angle_refined_deg1.356
r_scangle_it1.069
r_mcbond_it0.894
r_scbond_it0.647
r_nbtor_refined0.308
r_nbd_refined0.212
r_symmetry_vdw_refined0.184
r_xyhbond_nbd_refined0.173
r_symmetry_hbond_refined0.151
r_chiral_restr0.087
r_metal_ion_refined0.084
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2071
Nucleic Acid Atoms
Solvent Atoms76
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
AMoREphasing