☰ Navigation Tabs
Crystal structure of YiiM from Geobacillus stearothermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O65
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.095M sodium citrate pH 5.6, 21% PEG 4000, 19% isopropanol, 5% glycerol
Crystal Properties Matthews coefficient Solvent content 2.33 47.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.42 α = 90 b = 51.526 β = 90 c = 94.21 γ = 90
Symmetry Space Group P 21 21 21
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 270 2015-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 1.00004 PAL/PLS 7A (6B, 6C1)
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 30 99.7 0.066 38.9 5.7 15858
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 2 2.07 0.5 4.8
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 1O65 2 30 14960 783 99.26 0.18714 0.18532 0.1895 0.22346 0.2195 RANDOM 38.907
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] 0.52 -1.62 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.056 r_dihedral_angle_4_deg 16.878 r_dihedral_angle_3_deg 15.783 r_dihedral_angle_1_deg 6.031 r_scangle_it 3.573 r_scbond_it 2.291 r_mcangle_it 1.491 r_angle_refined_deg 1.44 r_angle_other_deg 0.907 r_mcbond_it 0.798
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.056 r_dihedral_angle_4_deg 16.878 r_dihedral_angle_3_deg 15.783 r_dihedral_angle_1_deg 6.031 r_scangle_it 3.573 r_scbond_it 2.291 r_mcangle_it 1.491 r_angle_refined_deg 1.44 r_angle_other_deg 0.907 r_mcbond_it 0.798 r_mcbond_other 0.197 r_chiral_restr 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001 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_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 1494 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-3000 data scaling PHASER phasing