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Crystal structure of YycF receiver domain from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A9R PDB ENTRY 2A9R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.2M Potassium sodium tartrate tetrahydrate, 0.1M tri-Sodium citrate dihydrate, 2.0M Ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.59 52.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.824 α = 90 b = 58.824 β = 90 c = 78.247 γ = 120
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 Bruker DIP-6040 2007-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 2.04 25.47 99.6 0.062 15.6 5.6 19218 19194 3 37
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) 2.04 2.15 100 0.417 3.7 5.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2A9R 2.04 25.47 19190 19190 935 99.6 0.1948 0.19543 0.19362 0.22982 0.2299 RANDOM 50.533
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] 1.33 0.66 1.33 -1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.043 r_dihedral_angle_4_deg 19.67 r_dihedral_angle_3_deg 15.651 r_dihedral_angle_1_deg 6.71 r_scangle_it 6.313 r_mcangle_it 4.38 r_scbond_it 3.813 r_mcbond_it 2.482 r_angle_refined_deg 1.886 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.043 r_dihedral_angle_4_deg 19.67 r_dihedral_angle_3_deg 15.651 r_dihedral_angle_1_deg 6.71 r_scangle_it 6.313 r_mcangle_it 4.38 r_scbond_it 3.813 r_mcbond_it 2.482 r_angle_refined_deg 1.886 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.254 r_nbd_refined 0.225 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.128 r_symmetry_hbond_refined 0.071 r_bond_refined_d 0.02 r_gen_planes_refined 0.006 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 1922 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing