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The cystal structure of the PDZ domain of human PICK1
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 5.5 293 0.2 M Ammonium-acetate, 0.1 M Bis-Tris, 20% PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.75 29.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.588 α = 90 b = 37.257 β = 95.75 c = 29.442 γ = 90
Symmetry Space Group C 1 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 MARRESEARCH mirrors 2006-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97925 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 1.12 29.3 98.4 0.0565 33346 32802
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 1.12 1.22 94.8 0.0126 7.97 3.04 7289
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 1.12 29.3 33346 31143 1659 98.49 0.15007 0.15007 0.14911 0.1577 0.16865 0.1694 RANDOM 9.872
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] -0.15 -0.11 -0.03 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.729 r_dihedral_angle_4_deg 23.812 r_dihedral_angle_3_deg 9.157 r_sphericity_free 6.72 r_dihedral_angle_1_deg 6.217 r_scangle_it 5.449 r_sphericity_bonded 4.632 r_scbond_it 4.356 r_mcangle_it 3.608 r_mcbond_it 3.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.729 r_dihedral_angle_4_deg 23.812 r_dihedral_angle_3_deg 9.157 r_sphericity_free 6.72 r_dihedral_angle_1_deg 6.217 r_scangle_it 5.449 r_sphericity_bonded 4.632 r_scbond_it 4.356 r_mcangle_it 3.608 r_mcbond_it 3.019 r_rigid_bond_restr 2.702 r_mcbond_other 2.445 r_angle_refined_deg 1.332 r_angle_other_deg 0.878 r_symmetry_vdw_other 0.238 r_nbd_refined 0.211 r_nbd_other 0.174 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.166 r_symmetry_hbond_refined 0.163 r_symmetry_vdw_refined 0.111 r_nbtor_other 0.092 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 667 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data scaling PHASER phasing