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Crystal structure of the S.cerevisiae Homing Endonuclease PI-SceI Domain I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VDE PDB ENTRY 1VDE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.8 30 % PEG4000, 0.1 M SODIUM CITRATE PH 5.6, 0.2 M NH4-ACETATE
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.856 α = 90 b = 47.595 β = 121.41 c = 60.297 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 IMAGE PLATE MARRESEARCH MIRRORS 2001-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 1.35 20 94.1 0.029 34.5 2.5 51602
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 1.35 1.37 64.1 0.164 2.5 1.5
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 1VDE 1.35 20 47840 3744 94.3 0.153 0.15 0.163 0.189 0.1997 RANDOM 19.93
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] -1.97 -0.61 1.92 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.1 r_scangle_it 5.758 r_dihedral_angle_1_deg 5.345 r_scbond_it 3.838 r_mcangle_it 2.979 r_mcbond_it 2.004 r_angle_refined_deg 1.834 r_angle_other_deg 0.952 r_symmetry_hbond_refined 0.44 r_nbd_refined 0.262
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.1 r_scangle_it 5.758 r_dihedral_angle_1_deg 5.345 r_scbond_it 3.838 r_mcangle_it 2.979 r_mcbond_it 2.004 r_angle_refined_deg 1.834 r_angle_other_deg 0.952 r_symmetry_hbond_refined 0.44 r_nbd_refined 0.262 r_symmetry_vdw_refined 0.245 r_xyhbond_nbd_refined 0.241 r_nbd_other 0.2 r_symmetry_vdw_other 0.192 r_chiral_restr 0.159 r_xyhbond_nbd_other 0.089 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_nbtor_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 1726 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing