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Crystal structure of the PDZ domain of human rhophilin-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F5Y PDB ENTRIES 2F5Y,2OCS,2V90 experimental model PDB 2OCS PDB ENTRIES 2F5Y,2OCS,2V90 experimental model PDB 2V90 PDB ENTRIES 2F5Y,2OCS,2V90
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.2M SODIUM ACETATE, 20% PEG3350; 10% ETHYLENE GLYCOL, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.1 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.25 α = 90 b = 39.89 β = 115.78 c = 73.48 γ = 90
Symmetry Space Group C 1 2 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 2008-03-09 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 1.82 38.9 99.1 0.1 8.8 3.4 18177 10.28
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 1.82 1.92 98.5 0.33 3.2 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRIES 2F5Y,2OCS,2V90 1.82 66.23 17238 939 98.8 0.222 0.22 0.2266 0.267 0.2774 RANDOM 12.21
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] 2.36 0.72 -0.39 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.622 r_dihedral_angle_4_deg 18.991 r_dihedral_angle_3_deg 12.525 r_scangle_it 9.236 r_scbond_it 6.724 r_dihedral_angle_1_deg 6.118 r_mcangle_it 4.101 r_mcbond_it 2.811 r_angle_refined_deg 1.376 r_angle_other_deg 0.902
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.622 r_dihedral_angle_4_deg 18.991 r_dihedral_angle_3_deg 12.525 r_scangle_it 9.236 r_scbond_it 6.724 r_dihedral_angle_1_deg 6.118 r_mcangle_it 4.101 r_mcbond_it 2.811 r_angle_refined_deg 1.376 r_angle_other_deg 0.902 r_nbd_refined 0.217 r_symmetry_vdw_other 0.202 r_nbd_other 0.19 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_refined 0.129 r_symmetry_vdw_refined 0.126 r_nbtor_other 0.087 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 1538 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing