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The crystal structure of the 13th PDZ domain of MPDZ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BYG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 8% PEG P3350, 0.1M acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.943 α = 90 b = 62.38 β = 106.26 c = 53.128 γ = 90
Symmetry Space Group P 1 21 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 2005-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97900 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 1.83 39.5 99.9 0.0508 26633 26605
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) 1.83 1.95 100 0.4753 2.15 4556
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 2byg 1.83 39.5 26633 26605 2038 99.97 0.19415 0.19415 0.19016 0.237 0.24293 0.2408 RANDOM 44.104
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] 0.21 0.06 0.05 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.366 r_dihedral_angle_4_deg 19.574 r_dihedral_angle_3_deg 14.272 r_scangle_it 8.016 r_dihedral_angle_1_deg 6.513 r_scbond_it 5.951 r_mcangle_it 4.243 r_mcbond_it 3.272 r_angle_refined_deg 1.556 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.366 r_dihedral_angle_4_deg 19.574 r_dihedral_angle_3_deg 14.272 r_scangle_it 8.016 r_dihedral_angle_1_deg 6.513 r_scbond_it 5.951 r_mcangle_it 4.243 r_mcbond_it 3.272 r_angle_refined_deg 1.556 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.264 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.175 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.119 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2175 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing