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CRYSTAL STRUCTURE ANALYSIS OF THE SECOND PDZ DOMAIN OF SYNTENIN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N99 PDB ENTRY 1N99
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 PEG 4000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 1.41 12.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.292 α = 90 b = 42.57 β = 108.71 c = 31.038 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 4 2002-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9B 0.97946 NSLS X9B
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 1.1 12.16 73.3 0.042 28.5 3.1 18559 18559 1 -3 7.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 1N99 1.24 12.16 1 16535 15684 851 93.13 0.11533 0.11325 0.1151 0.15331 0.1543 RANDOM 10.391
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] 0.04 0.26 -0.18 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.398 r_sphericity_free 5.089 r_scangle_it 3.372 r_sphericity_bonded 3.222 r_scbond_it 2.474 r_mcangle_it 1.956 r_angle_other_deg 1.885 r_angle_refined_deg 1.626 r_mcbond_it 1.312 r_rigid_bond_restr 1.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.398 r_sphericity_free 5.089 r_scangle_it 3.372 r_sphericity_bonded 3.222 r_scbond_it 2.474 r_mcangle_it 1.956 r_angle_other_deg 1.885 r_angle_refined_deg 1.626 r_mcbond_it 1.312 r_rigid_bond_restr 1.271 r_symmetry_vdw_other 0.332 r_xyhbond_nbd_refined 0.254 r_nbd_other 0.252 r_nbd_refined 0.246 r_symmetry_hbond_refined 0.184 r_chiral_restr 0.115 r_symmetry_vdw_refined 0.103 r_nbtor_other 0.085 r_gen_planes_other 0.019 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 608 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing