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CRYSTAL STRUCTURE OF a YbjQ-like protein of unknown function (SSO2532) FROM SULFOLOBUS SOLFATARICUS P2 AT 1.76 A RESOLUTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VMF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 7.5 277 10.0% iso-Propanol, 20.0% PEG-4000, 0.1M HEPES pH7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.13 41.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.86 α = 90 b = 92.18 β = 90 c = 114.13 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 ADSC QUANTUM 315 2004-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.764 28.68 90.9 0.062 15.6 3.9 75897 31.06
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.764 1.86 63.6 0.312 3 1.9 7634
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 (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 1VMF 1.764 16.22 72013 3791 90.69 0.19082 0.18914 0.1962 0.22173 0.229 RANDOM 22.167
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] 0.58 -2.01 1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.54 r_dihedral_angle_3_deg 14.27 r_dihedral_angle_4_deg 11.353 r_scangle_it 6.712 r_dihedral_angle_1_deg 6.46 r_scbond_it 4.767 r_mcangle_it 2.714 r_angle_refined_deg 1.607 r_mcbond_it 1.599 r_angle_other_deg 0.961
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.54 r_dihedral_angle_3_deg 14.27 r_dihedral_angle_4_deg 11.353 r_scangle_it 6.712 r_dihedral_angle_1_deg 6.46 r_scbond_it 4.767 r_mcangle_it 2.714 r_angle_refined_deg 1.607 r_mcbond_it 1.599 r_angle_other_deg 0.961 r_metal_ion_refined 0.479 r_mcbond_other 0.371 r_nbd_refined 0.272 r_symmetry_vdw_other 0.267 r_nbd_other 0.202 r_nbtor_refined 0.182 r_symmetry_vdw_refined 0.165 r_symmetry_hbond_refined 0.15 r_xyhbond_nbd_refined 0.148 r_xyhbond_nbd_other 0.128 r_chiral_restr 0.1 r_nbtor_other 0.09 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6658 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 64
Software Software Software Name Purpose SOLVE phasing SCALA data scaling MOLREP phasing REFMAC refinement CCP4 data scaling