1NZO

The crystal structure of wild type penicillin-binding protein 5 from E. coli


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HD8PDB ENTRY 1HD8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7294100mM Tris pH 7.0, 8% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.550.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.35α = 90
b = 50.28β = 120.9
c = 84.53γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVmirrors2002-01-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
11.855493.40.067.44.5316243162429.4
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)
1.851.9267.80.323242269

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1HD81.8514.923038430384154293.40.209640.209640.207790.24503RANDOM31.949
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]
-0.01-0.08-0.03-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg16.067
r_dihedral_angle_1_deg4.021
r_scangle_it3.264
r_scbond_it2.106
r_angle_refined_deg1.509
r_mcangle_it1.294
r_symmetry_hbond_refined0.812
r_mcbond_it0.717
r_symmetry_vdw_refined0.258
r_nbd_refined0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg16.067
r_dihedral_angle_1_deg4.021
r_scangle_it3.264
r_scbond_it2.106
r_angle_refined_deg1.509
r_mcangle_it1.294
r_symmetry_hbond_refined0.812
r_mcbond_it0.717
r_symmetry_vdw_refined0.258
r_nbd_refined0.24
r_xyhbond_nbd_refined0.195
r_chiral_restr0.107
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2718
Nucleic Acid Atoms
Solvent Atoms190
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
AMoREphasing