☰ Navigation Tabs
The crystal structure of the 10th PDZ domain of MPDZ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FNE PDB entry 2FNE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1M BIS-TRIS, 20% mPEG 5000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.46 48.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.944 α = 90 b = 54.944 β = 90 c = 118.355 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2006-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97880 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.5 39.47 99.9 0.068 19.2 8.4 33890 33890
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.58 99.6 0.455 7.3 4827
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2FNE 1.5 39.47 32150 32150 1718 99.81 0.17473 0.17473 0.17244 0.1919 0.21718 0.2375 RANDOM 18.291
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] 0.27 0.13 0.27 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.58 r_dihedral_angle_4_deg 19.421 r_dihedral_angle_3_deg 12.734 r_scangle_it 7.195 r_dihedral_angle_1_deg 6.56 r_scbond_it 5.291 r_mcangle_it 3.903 r_mcbond_it 2.537 r_angle_refined_deg 1.929 r_angle_other_deg 1.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.58 r_dihedral_angle_4_deg 19.421 r_dihedral_angle_3_deg 12.734 r_scangle_it 7.195 r_dihedral_angle_1_deg 6.56 r_scbond_it 5.291 r_mcangle_it 3.903 r_mcbond_it 2.537 r_angle_refined_deg 1.929 r_angle_other_deg 1.332 r_mcbond_other 0.754 r_symmetry_vdw_other 0.358 r_symmetry_vdw_refined 0.266 r_symmetry_hbond_refined 0.241 r_nbd_other 0.218 r_nbd_refined 0.198 r_chiral_restr 0.192 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.173 r_nbtor_other 0.09 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1529 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing