☰ Navigation Tabs
Structural insights into yeast Nit2: wild-type yeast Nit2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EMS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 287 17.5% PEG4000, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties Matthews coefficient Solvent content 2.06 40.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.262 α = 90 b = 125.665 β = 95.23 c = 77.674 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 RAYONIX MX-225 2010-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97792 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.91 50 100 95100 95100 4.66
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 1.91 1.94 100 0.348 4.81 3.7 4714
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 1EMS 1.92 48 95100 90290 4767 99.69 0.1724 0.1724 0.17078 0.1716 0.20228 0.2032 RANDOM 15.828
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] -0.75 -0.03 0.52 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.617 r_dihedral_angle_4_deg 14.118 r_dihedral_angle_3_deg 12.946 r_dihedral_angle_1_deg 5.805 r_scangle_it 2.135 r_scbond_it 1.237 r_angle_refined_deg 1.1597 r_mcangle_it 0.886 r_mcbond_it 0.477 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.617 r_dihedral_angle_4_deg 14.118 r_dihedral_angle_3_deg 12.946 r_dihedral_angle_1_deg 5.805 r_scangle_it 2.135 r_scbond_it 1.237 r_angle_refined_deg 1.1597 r_mcangle_it 0.886 r_mcbond_it 0.477 r_chiral_restr 0.077 r_bond_refined_d 0.0131 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9441 Nucleic Acid Atoms Solvent Atoms 784 Heterogen Atoms 83
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling