2OCS

The crystal structure of the first PDZ domain of human NHERF-2 (SLC9A3R2)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelSwissModelswissmodel generated model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529820% PEG 3350, 0.20M KSCN, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9336.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 26.556α = 90
b = 39.867β = 106.93
c = 37.278γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.535.661000.06560.0512.683.671206212057
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.51.61000.45950.3225.43.642093

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 REPLACEMENTTHROUGHOUTswissmodel generated model1.535.66120621144860999.960.154110.154110.151850.19829RANDOM14.108
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]
-0.290.03-0.630.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.583
r_dihedral_angle_4_deg17.97
r_dihedral_angle_3_deg12.38
r_sphericity_free9.877
r_dihedral_angle_1_deg6.303
r_scangle_it6.052
r_sphericity_bonded5.218
r_scbond_it4.131
r_mcangle_it3.173
r_mcbond_it2.188
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.583
r_dihedral_angle_4_deg17.97
r_dihedral_angle_3_deg12.38
r_sphericity_free9.877
r_dihedral_angle_1_deg6.303
r_scangle_it6.052
r_sphericity_bonded5.218
r_scbond_it4.131
r_mcangle_it3.173
r_mcbond_it2.188
r_rigid_bond_restr2.077
r_angle_refined_deg1.941
r_angle_other_deg1.222
r_mcbond_other1.062
r_symmetry_vdw_refined0.397
r_symmetry_vdw_other0.382
r_chiral_restr0.377
r_nbd_refined0.276
r_nbd_other0.235
r_xyhbond_nbd_refined0.188
r_nbtor_refined0.177
r_symmetry_hbond_refined0.161
r_nbtor_other0.092
r_bond_refined_d0.021
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms664
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
PHASERphasing