1W57

Structure of the Bifunctional IspDF from Campylobacter jejuni containing Zn


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W55PDB ENTRY 1W55

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
135 % ETHYLENE GLYCOL
Crystal Properties
Matthews coefficientSolvent content
3.262.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.76α = 90
b = 107.76β = 90
c = 161.004γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray160CCDADSC CCDTOROIDAL MIRROR2002-06-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12.3201000.0941.731.436758881.4
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)
13.13.211000.528.4

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 1W553.0995.353675885091000.2210.2170.295RANDOM38.71
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]
4.7892.3944.789-7.183
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it3.787
r_scbond_it2.462
r_angle_refined_deg2.128
r_angle_other_deg2.124
r_mcangle_it2.007
r_mcbond_it1.134
r_symmetry_vdw_other0.368
r_symmetry_hbond_refined0.316
r_nbd_other0.268
r_symmetry_vdw_refined0.238
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it3.787
r_scbond_it2.462
r_angle_refined_deg2.128
r_angle_other_deg2.124
r_mcangle_it2.007
r_mcbond_it1.134
r_symmetry_vdw_other0.368
r_symmetry_hbond_refined0.316
r_nbd_other0.268
r_symmetry_vdw_refined0.238
r_nbd_refined0.232
r_nbtor_refined0.201
r_xyhbond_nbd_refined0.193
r_chiral_restr0.142
r_nbtor_other0.105
r_bond_refined_d0.038
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
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 Atoms2908
Nucleic Acid Atoms
Solvent Atoms57
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing