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Crystal structure of a dinb-like protein (yjoa, bsu12410) from bacillus subtilis at 2.30 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 277 0.2000M NH4OAc, 30.0000% PEG-4000, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.07 40.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.69 α = 90 b = 63.34 β = 90 c = 82.06 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2008-05-14 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97956,0.97904 SSRL BL11-1
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 29.566 95.9 0.097 7.3 3.63 13596 -3 34.972
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 2.3 2.38 90.5 0.571 1.58
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 MAD THROUGHOUT 2.3 29.566 13568 677 97.56 0.219 0.217 0.2199 0.269 0.2723 RANDOM 27.26
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] 2.39 -0.47 -1.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.959 r_dihedral_angle_3_deg 13.55 r_dihedral_angle_4_deg 10.103 r_scangle_it 4.632 r_dihedral_angle_1_deg 4.557 r_scbond_it 3.402 r_mcangle_it 2.082 r_mcbond_it 1.304 r_angle_refined_deg 1.073 r_angle_other_deg 0.839
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.959 r_dihedral_angle_3_deg 13.55 r_dihedral_angle_4_deg 10.103 r_scangle_it 4.632 r_dihedral_angle_1_deg 4.557 r_scbond_it 3.402 r_mcangle_it 2.082 r_mcbond_it 1.304 r_angle_refined_deg 1.073 r_angle_other_deg 0.839 r_symmetry_hbond_refined 0.243 r_symmetry_vdw_other 0.225 r_mcbond_other 0.211 r_nbd_refined 0.192 r_nbtor_refined 0.172 r_nbd_other 0.17 r_xyhbond_nbd_refined 0.142 r_symmetry_vdw_refined 0.105 r_nbtor_other 0.087 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2288 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing