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Crystal structure of 2nd PDZ domain of glutamate receptor interacting protein-1 (GRIP1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N7E PDB ENTRY 1N7E 1TQ3 1BE9 1MFG 2HE2 1N7F experimental model PDB 1TQ3 PDB ENTRY 1N7E 1TQ3 1BE9 1MFG 2HE2 1N7F experimental model PDB 1BE9 PDB ENTRY 1N7E 1TQ3 1BE9 1MFG 2HE2 1N7F experimental model PDB 1MFG PDB ENTRY 1N7E 1TQ3 1BE9 1MFG 2HE2 1N7F experimental model PDB 2HE2 PDB ENTRY 1N7E 1TQ3 1BE9 1MFG 2HE2 1N7F experimental model PDB 1N7F PDB ENTRY 1N7E 1TQ3 1BE9 1MFG 2HE2 1N7F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 20% PEG3350, 0.20M POTASSIUM THIOCYANATE, 10% ETHYLENE GLYCOL, 0.1M BIS TRIS PROPANE PH 7.5
Crystal Properties Matthews coefficient Solvent content 1.98 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.06 α = 90 b = 61.057 β = 90 c = 96.397 γ = 90
Symmetry Space Group C 2 2 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 2007-05-10 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 1.5 41.31 99.9 0.06 16 4.2 26857 21.03
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 1.5 1.58 99.7 0.56 1.6 3.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1N7E 1TQ3 1BE9 1MFG 2HE2 1N7F 1.5 48.22 24603 2226 99.8 0.192 0.189 0.228 0.3077 RANDOM 17.94
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] 0.89 0.19 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.306 r_dihedral_angle_4_deg 20.649 r_dihedral_angle_3_deg 13.705 r_scangle_it 8.437 r_scbond_it 6.146 r_dihedral_angle_1_deg 5.92 r_mcangle_it 4.035 r_mcbond_it 2.646 r_angle_other_deg 1.678 r_angle_refined_deg 1.519
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.306 r_dihedral_angle_4_deg 20.649 r_dihedral_angle_3_deg 13.705 r_scangle_it 8.437 r_scbond_it 6.146 r_dihedral_angle_1_deg 5.92 r_mcangle_it 4.035 r_mcbond_it 2.646 r_angle_other_deg 1.678 r_angle_refined_deg 1.519 r_symmetry_vdw_other 0.377 r_symmetry_vdw_refined 0.367 r_nbd_refined 0.264 r_nbd_other 0.228 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.139 r_nbtor_other 0.087 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.004 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 1411 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing