5AZP

Crystal structure of a membrane protein from Pseudomonas aeruginosa


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5AZO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5293PEG 4000, sodium acetate, sodium formate
Crystal Properties
Matthews coefficientSolvent content
4.5572.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 257.515α = 90
b = 257.515β = 90
c = 81.825γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2015-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.90000SPring-8BL44XU

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
11.695099.522.93.6297648

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 REPLACEMENTTHROUGHOUT5AZO1.69502826141503399.40.161090.160080.17974RANDOM26.502
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]
-0.05-0.050.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.095
r_dihedral_angle_4_deg19.251
r_dihedral_angle_3_deg12.465
r_long_range_B_other9.01
r_long_range_B_refined9.009
r_dihedral_angle_1_deg5.04
r_scangle_other4.644
r_scbond_it3.08
r_scbond_other3.079
r_mcangle_it2.155
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.095
r_dihedral_angle_4_deg19.251
r_dihedral_angle_3_deg12.465
r_long_range_B_other9.01
r_long_range_B_refined9.009
r_dihedral_angle_1_deg5.04
r_scangle_other4.644
r_scbond_it3.08
r_scbond_other3.079
r_mcangle_it2.155
r_mcangle_other2.155
r_angle_refined_deg1.973
r_mcbond_it1.523
r_mcbond_other1.494
r_angle_other_deg1.097
r_chiral_restr0.125
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10290
Nucleic Acid Atoms
Solvent Atoms1885
Heterogen Atoms379

Software

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