☰ Navigation Tabs
2nd PDZ Domain of Discs Large Homologue 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PDR PDB ENTRY 1PDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 25% PEG 3350, 0.2M NACL, 0.1M BIS-TRIS PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.2 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.774 α = 90 b = 69.081 β = 90 c = 73.967 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU-MSC OSMIC MIRRORS 2005-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E
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 1.85 34.54 98.7 0.04 19.9 4.1 9967
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 1.85 1.95 91.4 0.34 2.2 2.1
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 1PDR 1.85 50.51 9195 754 98.2 0.2 0.196 0.2043 0.252 0.2607 RANDOM 35.84
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] 1.67 0.11 -1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.338 r_dihedral_angle_3_deg 12.176 r_scangle_it 8.567 r_scbond_it 6.806 r_dihedral_angle_1_deg 5.644 r_dihedral_angle_4_deg 4.929 r_mcangle_it 4.42 r_mcbond_it 3.552 r_angle_refined_deg 1.276 r_angle_other_deg 0.704
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.338 r_dihedral_angle_3_deg 12.176 r_scangle_it 8.567 r_scbond_it 6.806 r_dihedral_angle_1_deg 5.644 r_dihedral_angle_4_deg 4.929 r_mcangle_it 4.42 r_mcbond_it 3.552 r_angle_refined_deg 1.276 r_angle_other_deg 0.704 r_nbd_refined 0.191 r_nbtor_refined 0.17 r_nbd_other 0.164 r_xyhbond_nbd_refined 0.161 r_symmetry_vdw_other 0.143 r_symmetry_hbond_refined 0.126 r_symmetry_vdw_refined 0.105 r_nbtor_other 0.078 r_chiral_restr 0.071 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_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_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 738 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing