1UNB

Deacetoxycephalosporin C synthase complexed with 2-oxoglutarate and ampicillin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RXFPDB ENTRY 1RXF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.51.75M AMMONIUM SULPHATE, 5MM 2-OXOGLUTARATE,0.1M HEPESPH7.5, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.2645.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.7α = 90
b = 106.7β = 90
c = 71.6γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2002-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I711MAX III711

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
11.531.4940.0645.545847
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)
11.51.551000.295

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 1RXF1.531.54004621321000.1910.1890.236RANDOM22.3
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]
-0.66-0.33-0.660.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.154
r_scangle_it5.169
r_scbond_it3.28
r_mcangle_it2.472
r_angle_refined_deg2.375
r_angle_other_deg1.943
r_mcbond_it1.464
r_symmetry_vdw_other0.294
r_nbd_other0.268
r_nbd_refined0.232
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.154
r_scangle_it5.169
r_scbond_it3.28
r_mcangle_it2.472
r_angle_refined_deg2.375
r_angle_other_deg1.943
r_mcbond_it1.464
r_symmetry_vdw_other0.294
r_nbd_other0.268
r_nbd_refined0.232
r_symmetry_hbond_refined0.222
r_xyhbond_nbd_refined0.181
r_chiral_restr0.145
r_symmetry_vdw_refined0.125
r_nbtor_other0.102
r_bond_refined_d0.026
r_bond_other_d0.023
r_gen_planes_other0.01
r_gen_planes_refined0.008
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 Atoms2233
Nucleic Acid Atoms
Solvent Atoms188
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling