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Crystal structure of Bacillus subtilis protein yhfP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 5% PEG4K, 0.1M BisTris, 0.16M MgCl2, 5% Glucose, 0.2M NAD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.74 54.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.219 α = 90 b = 133.546 β = 90 c = 166.335 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 MARRESEARCH Vertical and Horizontal focusing mirrors 2004-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.979 APS 31-ID
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 20 0.128 7 408512 408512 -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) 2.7 20 99.1 0.128 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.7 20 61904 58764 3148 98.71 0.19111 0.19111 0.18729 0.26192 0.3059 RANDOM 29.932
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] 0.76 3.03 -3.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.097 r_dihedral_angle_3_deg 21.57 r_dihedral_angle_4_deg 19.491 r_sphericity_free 14.127 r_dihedral_angle_1_deg 8.293 r_scangle_it 6.901 r_mcangle_it 5.064 r_scbond_it 4.55 r_sphericity_bonded 4.478 r_rigid_bond_restr 3.536
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.097 r_dihedral_angle_3_deg 21.57 r_dihedral_angle_4_deg 19.491 r_sphericity_free 14.127 r_dihedral_angle_1_deg 8.293 r_scangle_it 6.901 r_mcangle_it 5.064 r_scbond_it 4.55 r_sphericity_bonded 4.478 r_rigid_bond_restr 3.536 r_mcbond_it 3.19 r_angle_refined_deg 3.006 r_nbtor_refined 0.354 r_nbd_refined 0.313 r_symmetry_vdw_refined 0.25 r_xyhbond_nbd_refined 0.24 r_chiral_restr 0.189 r_symmetry_hbond_refined 0.184 r_bond_refined_d 0.035 r_gen_planes_refined 0.01 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_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14617 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing