☰ Navigation Tabs
Crystal structure of the ygdR protein from E.coli. Northeast Structural Genomics target ER382A.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RB6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 12% PEG400, 0.1M Na-Acetate,
0.1M KH2PO4, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.96 37.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.017 α = 99.95 b = 41.056 β = 102.33 c = 73.748 γ = 104.4
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 MAR CCD 165 mm 2007-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.979 NSLS X4C
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 2.7 30 94.6 0.039 21.1 2.1 453287 22734 -3
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 2.7 2.8 97.6 0.059 13.5 2.2
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 2RB6 2.7 20 11125 555 100 0.23871 0.23802 0.2366 0.25253 0.2506 RANDOM 17.871
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] 0.4 0.76 -0.44 -0.38 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.168 r_dihedral_angle_4_deg 21.744 r_dihedral_angle_3_deg 14.975 r_dihedral_angle_1_deg 3.027 r_angle_refined_deg 1.229 r_scangle_it 1.15 r_scbond_it 0.754 r_mcangle_it 0.44 r_mcbond_it 0.383 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.168 r_dihedral_angle_4_deg 21.744 r_dihedral_angle_3_deg 14.975 r_dihedral_angle_1_deg 3.027 r_angle_refined_deg 1.229 r_scangle_it 1.15 r_scbond_it 0.754 r_mcangle_it 0.44 r_mcbond_it 0.383 r_nbtor_refined 0.315 r_nbd_refined 0.25 r_symmetry_vdw_refined 0.239 r_symmetry_hbond_refined 0.187 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3558 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection BALBES phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling