1W28

Conformational flexibility of the C-terminus with implications for substrate binding and catalysis in a new crystal form of deacetoxycephalosporin C synthase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DCSPDB ENTRY 1DCS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18100 MM HEPES-NAOH PH 8, 0.9-1.1 M AMSO4
Crystal Properties
Matthews coefficientSolvent content
4.170

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138α = 90
b = 138β = 90
c = 48.4γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
12.34599.40.0432423763
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)
12.32.3898.40.313.63

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 1DCS2.345.1822412118999.40.1980.1970.223RANDOM39.56
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]
0.010.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.146
r_scangle_it3.366
r_scbond_it1.961
r_mcangle_it1.356
r_angle_refined_deg1.288
r_angle_other_deg0.799
r_mcbond_it0.706
r_symmetry_vdw_other0.306
r_symmetry_vdw_refined0.249
r_nbd_other0.235
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.146
r_scangle_it3.366
r_scbond_it1.961
r_mcangle_it1.356
r_angle_refined_deg1.288
r_angle_other_deg0.799
r_mcbond_it0.706
r_symmetry_vdw_other0.306
r_symmetry_vdw_refined0.249
r_nbd_other0.235
r_nbd_refined0.214
r_xyhbond_nbd_refined0.178
r_symmetry_hbond_refined0.175
r_nbtor_other0.085
r_chiral_restr0.075
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2109
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing