4OJ8

Crystal structure of carbapenem synthase in complex with (3S,5S)-carbapenam


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NX4PDB ENTRY 1NX4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298HEPES, isopropanol, ammonium acetate, pH 7.0, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.448.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.251α = 90
b = 165.778β = 90
c = 146.58γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2012-11-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97857APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.157198

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 1NX42.13057198289199.710.20010.19830.2357RANDOM45.237
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]
2.560.11-2.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.241
r_dihedral_angle_4_deg15.266
r_dihedral_angle_3_deg12.757
r_dihedral_angle_1_deg5.696
r_mcangle_it1.517
r_scbond_it1.071
r_angle_refined_deg0.98
r_mcbond_it0.927
r_chiral_restr0.07
r_bond_refined_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.241
r_dihedral_angle_4_deg15.266
r_dihedral_angle_3_deg12.757
r_dihedral_angle_1_deg5.696
r_mcangle_it1.517
r_scbond_it1.071
r_angle_refined_deg0.98
r_mcbond_it0.927
r_chiral_restr0.07
r_bond_refined_d0.005
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6519
Nucleic Acid Atoms
Solvent Atoms411
Heterogen Atoms61

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling