3ZOJ

High-resolution structure of Pichia Pastoris aquaporin Aqy1 at 0.88 A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2W2EPDB ENTRY 2W2E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1826% PEG600, 100 MM TRIS (PH=8.0), 200 MM CACL2
Crystal Properties
Matthews coefficientSolvent content
2.7755.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.763α = 90
b = 90.763β = 90
c = 80.311γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMIRRORS2010-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
10.88641000.0626.213.8252057-3
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)
10.880.931000.872.811

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 2W2E0.8860.15249442238199.830.103290.103250.10739RANDOM10.806
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]
-0.04-0.040.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.08
r_dihedral_angle_4_deg19.084
r_sphericity_free16.265
r_dihedral_angle_3_deg11.485
r_sphericity_bonded8.006
r_rigid_bond_restr5.423
r_dihedral_angle_1_deg4.921
r_scbond_it1.692
r_angle_refined_deg1.691
r_mcangle_it1.055
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.08
r_dihedral_angle_4_deg19.084
r_sphericity_free16.265
r_dihedral_angle_3_deg11.485
r_sphericity_bonded8.006
r_rigid_bond_restr5.423
r_dihedral_angle_1_deg4.921
r_scbond_it1.692
r_angle_refined_deg1.691
r_mcangle_it1.055
r_mcbond_it0.901
r_mcbond_other0.873
r_angle_other_deg0.872
r_chiral_restr0.096
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2001
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling