☰ Navigation Tabs
Structure-based functional annotation: Yeast ymr099c codes for a D- hexose-6-phosphate mutarotase. Complex with glucose-6-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CIQ PDB ENTRY 2CIQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 32% POLYETHYLENE GLYCOL 4000, 0.2 M LITHIUM CHLORIDE, 0.1M HEPES PH 7.5.
Crystal Properties Matthews coefficient Solvent content 2.8 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.63 α = 90 b = 157.067 β = 90 c = 104.024 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 100 CCD ADSC CCD 2005-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.5 20 98.9 0.08 21.5 4.3 57846 2
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 1.5 1.6 99.6 0.46 2.5
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 2CIQ 1.6 20 44062 2376 97.5 0.208 0.206 0.2021 0.234 0.2288 RANDOM 21.96
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] 1.62 -1.21 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.154 r_dihedral_angle_3_deg 13.303 r_dihedral_angle_4_deg 12.227 r_dihedral_angle_1_deg 6.162 r_scangle_it 3.404 r_scbond_it 2.753 r_mcangle_it 1.668 r_angle_refined_deg 1.307 r_mcbond_it 1.095 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.154 r_dihedral_angle_3_deg 13.303 r_dihedral_angle_4_deg 12.227 r_dihedral_angle_1_deg 6.162 r_scangle_it 3.404 r_scbond_it 2.753 r_mcangle_it 1.668 r_angle_refined_deg 1.307 r_mcbond_it 1.095 r_nbtor_refined 0.309 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.129 r_symmetry_vdw_refined 0.129 r_chiral_restr 0.091 r_symmetry_hbond_refined 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 2321 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing