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CRYSTAL STRUCTURE OF THE FIRST PDZ DOMAIN OF HUMAN SCRIB1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X5Q PDB ENTRY 1X5Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.3 0.15 M AMMONIUM CL PH 6.3, 20 % PEG 1000, 15% ETHYLENE GLYCOL
Crystal Properties Matthews coefficient Solvent content 1.95 37.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.216 α = 90 b = 41.829 β = 90 c = 49.897 γ = 90
Symmetry Space Group P 21 21 21
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 2008-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 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 1.3 41.81 99.8 0.05 14.5 3.5 71804 4.6 14.4
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 1.3 1.37 100 0.26 4.6 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1X5Q 1.3 24.94 19190 1028 99.7 0.175 0.173 0.1821 0.221 0.2241 RANDOM 13.92
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] -0.11 -0.24 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.615 r_dihedral_angle_3_deg 12.456 r_dihedral_angle_4_deg 11.021 r_scangle_it 8.47 r_scbond_it 6.132 r_dihedral_angle_1_deg 5.586 r_mcangle_it 4.556 r_mcbond_it 3.293 r_angle_refined_deg 1.38 r_angle_other_deg 0.878
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.615 r_dihedral_angle_3_deg 12.456 r_dihedral_angle_4_deg 11.021 r_scangle_it 8.47 r_scbond_it 6.132 r_dihedral_angle_1_deg 5.586 r_mcangle_it 4.556 r_mcbond_it 3.293 r_angle_refined_deg 1.38 r_angle_other_deg 0.878 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 689 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing