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The structure of GIY-YIG endonuclease R.Eco29kI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other MAD, phase information by PHENIX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1M Tris HCl, 1.5M NaCl, 10% ethanol v/v, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.28 62.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.906 α = 90 b = 90.074 β = 90 c = 88.85 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 110 CCD ADSC QUANTUM 315 2009-07-29 M SINGLE WAVELENGTH 2 1 x-ray CCD ADSC QUANTUM 315 2009-10-28 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0 ALS 5.0.1 2 SYNCHROTRON ALS BEAMLINE 5.0.2 0.9801, 0.9802, 0.975 ALS 5.0.2
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 2.3 62.91 98.82 0.079 18.35 4.9 15893 15078
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) 2.3 2.358 94.2 0.311 4.2 4.5
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT Phase information by PHENIX 2.3 50 15893 15078 791 98.82 0.18507 0.18285 0.2003 0.22781 0.2498 RANDOM 42.06
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] 0.62 1.97 -2.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.557 r_dihedral_angle_3_deg 15.522 r_dihedral_angle_4_deg 14.827 r_dihedral_angle_1_deg 7.659 r_scangle_it 5.291 r_scbond_it 3.38 r_mcangle_it 2.346 r_angle_refined_deg 1.951 r_mcbond_it 1.279 r_chiral_restr 0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.557 r_dihedral_angle_3_deg 15.522 r_dihedral_angle_4_deg 14.827 r_dihedral_angle_1_deg 7.659 r_scangle_it 5.291 r_scbond_it 3.38 r_mcangle_it 2.346 r_angle_refined_deg 1.951 r_mcbond_it 1.279 r_chiral_restr 0.139 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1640 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHENIX model building REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHENIX phasing