3A3D

Crystal structure of penicillin binding protein 4 (dacB) from Haemophilus influenzae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EX2PDB ENTRY 2EX2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1M HEPES pH 7.5, 25% (w/v) PEG 6000, 5% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
358.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.548α = 90
b = 92.59β = 107.75
c = 104.882γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon FactoryBL-5A

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
11.62094.90.0624146613
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)
11.61.6684.90.26

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 2EX21.619.9813925573461000.172530.170890.20408RANDOM20.209
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]
-0.35-0.120.150.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.179
r_dihedral_angle_4_deg23.155
r_dihedral_angle_3_deg13.636
r_dihedral_angle_1_deg6.213
r_scangle_it6.196
r_scbond_it3.943
r_angle_refined_deg2.547
r_mcangle_it2.526
r_mcbond_it1.531
r_chiral_restr0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.179
r_dihedral_angle_4_deg23.155
r_dihedral_angle_3_deg13.636
r_dihedral_angle_1_deg6.213
r_scangle_it6.196
r_scbond_it3.943
r_angle_refined_deg2.547
r_mcangle_it2.526
r_mcbond_it1.531
r_chiral_restr0.2
r_bond_refined_d0.031
r_gen_planes_refined0.015
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7012
Nucleic Acid Atoms
Solvent Atoms924
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing