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Crystal Structure of the B. subtilis YkuD protein at 2 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.9 294.1 PEG 3350, acetate, lithium sulfate, cadmium chloride, pH 4.9, VAPOR DIFFUSION, SITTING DROP, temperature 294.1K, pH 4.90
Crystal Properties Matthews coefficient Solvent content 2.4 48.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.276 α = 90 b = 63.91 β = 90 c = 93.679 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 77.3 CCD ADSC QUANTUM 4 2004-04-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9B 0.97946, 0.97919, 0.97178 NSLS X9B
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 2.05 30 99.1 0.057 15.5 2.2 21805 2
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) 2.05 2.12 99 0.459 2.8 2.2
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.05 30 21805 20691 1114 99.8 0.214 0.211 0.2536 0.27 0.3033 RANDOM 23.6
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] 4.23 -1.75 -2.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.449 r_scangle_it 2.9 r_scbond_it 1.872 r_angle_refined_deg 1.441 r_mcangle_it 0.968 r_angle_other_deg 0.854 r_mcbond_it 0.548 r_nbd_other 0.237 r_symmetry_vdw_other 0.225 r_nbd_refined 0.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.449 r_scangle_it 2.9 r_scbond_it 1.872 r_angle_refined_deg 1.441 r_mcangle_it 0.968 r_angle_other_deg 0.854 r_mcbond_it 0.548 r_nbd_other 0.237 r_symmetry_vdw_other 0.225 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.204 r_xyhbond_nbd_refined 0.189 r_symmetry_vdw_refined 0.184 r_chiral_restr 0.09 r_nbtor_other 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2468 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SHARP phasing