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The crystal structure of the ydeN gene product from B. subtilis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 20% PEG 8000, 0.05 M KH2PO4, PH 4.6
Crystal Properties Matthews coefficient Solvent content 2.1 40.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.128 α = 90 b = 53.971 β = 90 c = 93.151 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 2003-10-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97920,0.97931,0.97546 APS 22-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 1.7 50 99.8 0.082 13.9 3.5 31784
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 1.83 1.91 65.8 0.22 4.3 2.3
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION OTHER THROUGHOUT 1.8 46.62 15495 1038 94.4 0.125 0.1285 0.181 0.1824 RANDOM 12.41
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] -0.71 1.03 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.271 r_scangle_it 4.619 r_scbond_it 3.115 r_mcangle_it 2.14 r_angle_other_deg 1.904 r_angle_refined_deg 1.621 r_mcbond_it 1.395 r_nbd_refined 0.324 r_symmetry_vdw_other 0.304 r_xyhbond_nbd_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.271 r_scangle_it 4.619 r_scbond_it 3.115 r_mcangle_it 2.14 r_angle_other_deg 1.904 r_angle_refined_deg 1.621 r_mcbond_it 1.395 r_nbd_refined 0.324 r_symmetry_vdw_other 0.304 r_xyhbond_nbd_refined 0.303 r_nbd_other 0.252 r_symmetry_hbond_refined 0.229 r_chiral_restr 0.108 r_nbtor_other 0.087 r_symmetry_vdw_refined 0.046 r_bond_refined_d 0.019 r_gen_planes_other 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 1493 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling SHELXD phasing SHARP phasing REFMAC refinement