3K1R

Structure of harmonin NPDZ1 in complex with the SAM-PBM of Sans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2KBQN-domain (PDB id:2KBQ), PDZ domain (PDB ID:1QAV), SAM domain (PDB ID 1KW4 and 1PK1)
experimental modelPDB 1QAVN-domain (PDB id:2KBQ), PDZ domain (PDB ID:1QAV), SAM domain (PDB ID 1KW4 and 1PK1)
experimental modelPDB 1KW4N-domain (PDB id:2KBQ), PDZ domain (PDB ID:1QAV), SAM domain (PDB ID 1KW4 and 1PK1)
experimental modelPDB 1PK1N-domain (PDB id:2KBQ), PDZ domain (PDB ID:1QAV), SAM domain (PDB ID 1KW4 and 1PK1)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52890.2M CaAc2, 0.1M HEPES, pH 7.5, 18% (w/v) polyethylene glycol 10000, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
3.2662.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.603α = 90
b = 57.775β = 104.63
c = 59.505γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2009-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU ULTRAX 181.5418

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
12.330.8930.08610.9162682224.1
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)
2.32.42930.0860.2110.9416268

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTN-domain (PDB id:2KBQ), PDZ domain (PDB ID:1QAV), SAM domain (PDB ID 1KW4 and 1PK1)2.328.893.3162681543082592.530.212620.210370.25568RANDOM25.719
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]
1.560.18-0.81-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.187
r_dihedral_angle_4_deg16.891
r_dihedral_angle_3_deg14.667
r_dihedral_angle_1_deg4.434
r_angle_refined_deg0.955
r_chiral_restr0.062
r_bond_refined_d0.006
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2139
Nucleic Acid Atoms
Solvent Atoms239
Heterogen Atoms

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASESphasing
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling