2VWR

Crystal structure of the second pdz domain of numb-binding protein 2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QG1PDB ENTRIES 2QG1 AND 2HE2
experimental modelPDB 2HE2PDB ENTRIES 2QG1 AND 2HE2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.240% PEG 300, 0.1M CITRATE/PO4 PH 4.2
Crystal Properties
Matthews coefficientSolvent content
2.0339.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.773α = 90
b = 38.643β = 117.22
c = 38.186γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2008-04-10MSINGLE 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)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
11.333.96980.06165.4199965.210.3
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)
11.31.3788.90.245.24.4

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 ENTRIES 2QG1 AND 2HE21.333.9618972102497.80.1360.1340.177RANDOM9.5
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]
-0.16-0.050.14-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.281
r_dihedral_angle_4_deg11.507
r_dihedral_angle_3_deg10.524
r_scangle_it9.761
r_scbond_it6.932
r_dihedral_angle_1_deg6.035
r_mcangle_it4.562
r_mcbond_it3.352
r_angle_refined_deg1.313
r_angle_other_deg0.876
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.281
r_dihedral_angle_4_deg11.507
r_dihedral_angle_3_deg10.524
r_scangle_it9.761
r_scbond_it6.932
r_dihedral_angle_1_deg6.035
r_mcangle_it4.562
r_mcbond_it3.352
r_angle_refined_deg1.313
r_angle_other_deg0.876
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.002
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms723
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing