7NZD

Fourth SH3 domain of POSH (Plenty of SH3 Domains protein)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2LJ1Homology model build with the template 2LJ1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.52930.1M MES pH 6.5, 23% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.52α = 90
b = 45.52β = 90
c = 65.74γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2020-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9119DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.4565.74100123.818.814475
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.4899.290.521

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEHomology model build with the template 2LJ11.4565.741444371699.8410.1640.16010.227537.451
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]
1.2740.6371.274-4.132
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.278
r_dihedral_angle_4_deg21.083
r_dihedral_angle_3_deg13.301
r_dihedral_angle_1_deg6.829
r_lrange_it6.782
r_lrange_other6.778
r_scangle_it6.603
r_scangle_other6.595
r_scbond_it5.426
r_scbond_other5.419
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.278
r_dihedral_angle_4_deg21.083
r_dihedral_angle_3_deg13.301
r_dihedral_angle_1_deg6.829
r_lrange_it6.782
r_lrange_other6.778
r_scangle_it6.603
r_scangle_other6.595
r_scbond_it5.426
r_scbond_other5.419
r_rigid_bond_restr4.449
r_mcangle_it4.05
r_mcangle_other4.048
r_mcbond_it3.584
r_mcbond_other3.342
r_angle_refined_deg1.501
r_angle_other_deg1.305
r_symmetry_nbd_refined0.461
r_nbd_other0.307
r_xyhbond_nbd_refined0.245
r_symmetry_nbd_other0.196
r_nbd_refined0.192
r_nbtor_refined0.167
r_symmetry_xyhbond_nbd_refined0.147
r_symmetry_nbtor_other0.079
r_chiral_restr0.072
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms511
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing