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CRYSTAL STRUCTURE OF a protein of the DUF1048 family with a left-handed superhelix fold (BH3976) FROM BACILLUS HALODURANS AT 1.95 A RESOLUTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O3L pdb enrty 2o3l
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 4.2 277 0.2M (NH4)2SO4, 10.0% Glycerol, 20.0% PEG-300, 0.1M Phosphate Citrate pH 4.2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.33 63.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.577 α = 90 b = 85.577 β = 90 c = 104.575 γ = 120
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 300 mm CCD Adjustable focusing mirrors in K-B geometry 2006-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.95 60.412 99.8 0.091 0.091 4.1 5.1 10900 35
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) 1 1.95 2 98.9 0.521 0.521 1.4 3.2 759
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MOLECULAR REPLACEMENT THROUGHOUT pdb enrty 2o3l 1.95 60.412 10898 523 99.75 0.205 0.205 0.203 0.2105 0.255 0.2595 RANDOM 43.239
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] 2.84 1.42 2.84 -4.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.084 r_dihedral_angle_3_deg 12.884 r_scangle_it 6.712 r_dihedral_angle_1_deg 5.75 r_scbond_it 5.26 r_mcangle_it 3.278 r_mcbond_it 2.502 r_angle_refined_deg 1.442 r_angle_other_deg 0.819 r_dihedral_angle_4_deg 0.682
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.084 r_dihedral_angle_3_deg 12.884 r_scangle_it 6.712 r_dihedral_angle_1_deg 5.75 r_scbond_it 5.26 r_mcangle_it 3.278 r_mcbond_it 2.502 r_angle_refined_deg 1.442 r_angle_other_deg 0.819 r_dihedral_angle_4_deg 0.682 r_mcbond_other 0.665 r_symmetry_vdw_refined 0.284 r_nbd_refined 0.237 r_xyhbond_nbd_refined 0.199 r_nbtor_refined 0.193 r_symmetry_vdw_other 0.173 r_symmetry_hbond_refined 0.164 r_nbd_other 0.161 r_chiral_restr 0.094 r_nbtor_other 0.088 r_xyhbond_nbd_other 0.035 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 686 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 14
Software Software Software Name Purpose MolProbity model building REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling MOLREP phasing