3B9W

The 1.3 A resolution structure of Nitrosomonas europaea Rh50 and mechanistic implications for NH3 transport by Rhesus family proteins


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NUUPDB Entrty 2NUU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529810mM Tris/HCl pH=8.5, 0.2M NaCl, 24% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.2462.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.061α = 90
b = 100.061β = 90
c = 143.828γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-03-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.07209SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.32099.80.0618.71131874-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.41000.682

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 Entrty 2NUU1.320125231663799.830.15090.148090.146920.17082RANDOM23.28
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]
0.150.080.15-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.435
r_dihedral_angle_3_deg11.261
r_sphericity_free10.532
r_dihedral_angle_4_deg10.411
r_scangle_it6.147
r_sphericity_bonded6.045
r_scbond_it4.712
r_dihedral_angle_1_deg4.598
r_mcangle_it3.493
r_mcbond_it2.848
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.435
r_dihedral_angle_3_deg11.261
r_sphericity_free10.532
r_dihedral_angle_4_deg10.411
r_scangle_it6.147
r_sphericity_bonded6.045
r_scbond_it4.712
r_dihedral_angle_1_deg4.598
r_mcangle_it3.493
r_mcbond_it2.848
r_rigid_bond_restr2.625
r_angle_refined_deg1.005
r_nbtor_refined0.303
r_nbd_refined0.19
r_symmetry_vdw_refined0.134
r_xyhbond_nbd_refined0.084
r_symmetry_hbond_refined0.081
r_chiral_restr0.075
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2671
Nucleic Acid Atoms
Solvent Atoms372
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing