8BLV

The PDZ domains of human SDCBP with a bound SDC4 C-terminal peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N99 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.3293200 mM sodium sulphate, 100 mM bis-tris-propane, 10% ethylene glycol, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2846.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.71α = 90
b = 67.462β = 90
c = 106.74γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
11.5106.741000.0330.99915.279.266371
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.532.2170.6580.6

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-VALUE1n991.557.02766190200699.8460.1830.18170.22232.561
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]
2.5610.349-2.909
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.831
r_dihedral_angle_3_deg13.715
r_dihedral_angle_2_deg9.876
r_lrange_other8.971
r_lrange_it8.97
r_scangle_it6.835
r_scangle_other6.834
r_dihedral_angle_1_deg6.716
r_mcangle_it5.54
r_mcangle_other5.539
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.831
r_dihedral_angle_3_deg13.715
r_dihedral_angle_2_deg9.876
r_lrange_other8.971
r_lrange_it8.97
r_scangle_it6.835
r_scangle_other6.834
r_dihedral_angle_1_deg6.716
r_mcangle_it5.54
r_mcangle_other5.539
r_scbond_it4.755
r_scbond_other4.754
r_mcbond_it3.821
r_mcbond_other3.82
r_angle_refined_deg1.729
r_angle_other_deg0.582
r_nbd_refined0.223
r_xyhbond_nbd_refined0.193
r_symmetry_nbd_other0.189
r_symmetry_xyhbond_nbd_refined0.18
r_nbtor_refined0.168
r_nbd_other0.165
r_symmetry_nbd_refined0.138
r_ncsr_local_group_10.127
r_symmetry_xyhbond_nbd_other0.12
r_chiral_restr0.09
r_symmetry_nbtor_other0.083
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2964
Nucleic Acid Atoms
Solvent Atoms345
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing