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Crystal structure of protein ypsA from Bacillus subtilis, Pfam DUF1273
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 18 % PEG-4K, Na-Acetate pH 4.6, Ammonium Acetate 0.1M, 0.1M, Ethylene Glycol 10%, Vapor diffusion, Sitting drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.13 42.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.052 α = 90 b = 51.052 β = 90 c = 138.22 γ = 90
Symmetry Space Group P 41 21 2
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 MAR CCD 165 mm M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 M SINGLE WAVELENGTH 3 1 x-ray 100 CCD MAR CCD 165 mm M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X3A 0.9793 NSLS X3A 2 SYNCHROTRON NSLS BEAMLINE X29A 1.7403 NSLS X29A 3 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 1,2,3 2 50 99.9 0.09 26.5 12.6 13121 13121
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 100 0.441 0.91 2.95 5.4 1260
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SIRAS THROUGHOUT 2 47.89 13060 637 99.98 0.182 0.18 0.1789 0.224 0.219 RANDOM 25.497
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] 0.54 0.54 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.9 r_dihedral_angle_4_deg 15.558 r_dihedral_angle_3_deg 14.7 r_dihedral_angle_1_deg 6.112 r_scangle_it 3.206 r_scbond_it 2.036 r_mcangle_it 1.449 r_angle_refined_deg 1.308 r_mcbond_it 0.857 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.9 r_dihedral_angle_4_deg 15.558 r_dihedral_angle_3_deg 14.7 r_dihedral_angle_1_deg 6.112 r_scangle_it 3.206 r_scbond_it 2.036 r_mcangle_it 1.449 r_angle_refined_deg 1.308 r_mcbond_it 0.857 r_nbtor_refined 0.306 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.181 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1505 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction HKL-2000 data scaling SHELXD phasing SHELXE model building