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Crystal structure of YrrB: a TPR protein with an unusual peptide-binding site
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.8 294 40MM PHOTASSIUM PHOSPHATE(KH2PO4), 4% PEG 6000, 20% GLYCEROL, PH 4.8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, pH 4.80
Crystal Properties Matthews coefficient Solvent content 2.1 40.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.938 α = 90 b = 85.139 β = 130.63 c = 69.048 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 210 2005-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A PAL/PLS 4A
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 2.49 30 95.1 0.091 3.9 14817 -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 2.49 2.59 76.7 0.243 2.6 2.5 1183
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.49 28.48 13328 1488 94.9 0.211 0.206 0.256 0.2624 RANDOM 59.84
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 0.05 -0.52 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.268 r_dihedral_angle_4_deg 20.48 r_dihedral_angle_3_deg 18.991 r_dihedral_angle_1_deg 4.844 r_scangle_it 1.776 r_scbond_it 1.043 r_mcangle_it 0.802 r_mcbond_it 0.435 r_nbtor_refined 0.303 r_nbd_refined 0.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.268 r_dihedral_angle_4_deg 20.48 r_dihedral_angle_3_deg 18.991 r_dihedral_angle_1_deg 4.844 r_scangle_it 1.776 r_scbond_it 1.043 r_mcangle_it 0.802 r_mcbond_it 0.435 r_nbtor_refined 0.303 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.097 r_chiral_restr 0.074 r_gen_planes_refined 0.003 r_bond_refined_d r_bond_other_d r_angle_refined_deg 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 3048 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms
Software Software Software Name Purpose SOLVE phasing REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling