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Crystal structure of the PDZ domain of human GRASP (GRP1) in complex with the C-terminal peptide of the metabotropic glutamate receptor type 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GQ4 PDB entries 1GQ4, 2OCS experimental model PDB 2OCS PDB entries 1GQ4, 2OCS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.7 298 1.26M NaH2PO4, 0.14M K2HPO4, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.79 55.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.288 α = 90 b = 72.288 β = 90 c = 163.311 γ = 120
Symmetry Space Group P 65 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 CCD MARMOSAIC 225 mm CCD 2007-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.035 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 2.148 62.622 100 0.091 8.8 14546 14546
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.148 2.23 99.9 6.5 1411
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 entries 1GQ4, 2OCS 2.148 62.62 13758 13758 729 99.91 0.20995 0.20995 0.20876 0.2236 0.23198 0.2427 RANDOM 34.719
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] 0.33 0.17 0.33 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.899 r_dihedral_angle_4_deg 23.675 r_dihedral_angle_3_deg 15.342 r_dihedral_angle_1_deg 7.072 r_scangle_it 3.934 r_scbond_it 2.54 r_mcangle_it 1.612 r_angle_refined_deg 1.517 r_angle_other_deg 0.923 r_mcbond_it 0.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.899 r_dihedral_angle_4_deg 23.675 r_dihedral_angle_3_deg 15.342 r_dihedral_angle_1_deg 7.072 r_scangle_it 3.934 r_scbond_it 2.54 r_mcangle_it 1.612 r_angle_refined_deg 1.517 r_angle_other_deg 0.923 r_mcbond_it 0.919 r_symmetry_vdw_refined 0.257 r_symmetry_vdw_other 0.255 r_symmetry_hbond_refined 0.226 r_mcbond_other 0.201 r_nbd_other 0.198 r_nbd_refined 0.197 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.097 r_nbtor_other 0.089 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1414 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing