2IWP

12th PDZ domain of Multiple PDZ Domain Protein MPDZ


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FNEPDB ENTRY 2FNE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.550% PEG 300, 0.2M LI2SO4, 0.1M ACETATE PH 4.5
Crystal Properties
Matthews coefficientSolvent content
2.4650.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.71α = 90
b = 88.099β = 90
c = 73.154γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-06-16MSINGLE 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
12.1557.8399.40.09113.713731
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)
12.152.271000.472.53.7

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 2FNE2.1557.831303368799.30.2230.2210.27RANDOM44.16
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]
0.253.14-3.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.92
r_dihedral_angle_4_deg25.274
r_dihedral_angle_3_deg18.474
r_dihedral_angle_1_deg7.141
r_scangle_it3.545
r_scbond_it2.194
r_angle_refined_deg1.608
r_mcangle_it1.399
r_angle_other_deg0.919
r_mcbond_it0.909
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.92
r_dihedral_angle_4_deg25.274
r_dihedral_angle_3_deg18.474
r_dihedral_angle_1_deg7.141
r_scangle_it3.545
r_scbond_it2.194
r_angle_refined_deg1.608
r_mcangle_it1.399
r_angle_other_deg0.919
r_mcbond_it0.909
r_symmetry_vdw_refined0.253
r_nbd_refined0.209
r_nbd_other0.207
r_nbtor_refined0.176
r_symmetry_vdw_other0.174
r_xyhbond_nbd_refined0.16
r_nbtor_other0.093
r_chiral_restr0.086
r_symmetry_hbond_refined0.062
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.001
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
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 Atoms1377
Nucleic Acid Atoms
Solvent Atoms24
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing