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Crystal structure of Bacillus caldolyticus cold shock protein in complex with hexathymidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C9O PDB entry 1C9O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293.15 35% 2-methyl-2,4-pentanediol, 0.1 M sodium acetate pH 4.6, 0.02 M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.06 40.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.34 α = 90 b = 64.89 β = 90 c = 31.2 γ = 90
Symmetry Space Group P 21 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 110 CCD MAR CCD 165 mm mirrors 2003-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 1.29 19.5 97.9 0.066 14.68 6.3 38879 38068 -3 -3 16.166
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) 1.29 1.5 95.1 0.239 6.1 6.2 13269
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 entry 1C9O 1.29 19.5 38036 36128 1908 95 0.132 0.132 0.13 0.1335 0.162 0.1678 RANDOM 10.87
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] -0.37 -0.25 0.62
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 14.831 r_sphericity_bonded 6.33 r_scangle_it 5.166 r_dihedral_angle_1_deg 4.346 r_scbond_it 3.878 r_mcangle_it 3.158 r_mcbond_it 2.177 r_angle_refined_deg 1.567 r_rigid_bond_restr 1.479 r_angle_other_deg 0.98
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 14.831 r_sphericity_bonded 6.33 r_scangle_it 5.166 r_dihedral_angle_1_deg 4.346 r_scbond_it 3.878 r_mcangle_it 3.158 r_mcbond_it 2.177 r_angle_refined_deg 1.567 r_rigid_bond_restr 1.479 r_angle_other_deg 0.98 r_symmetry_vdw_other 0.309 r_nbd_other 0.263 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.203 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.096 r_nbtor_other 0.086 r_bond_refined_d 0.018 r_gen_planes_other 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1117 Nucleic Acid Atoms 246 Solvent Atoms 250 Heterogen Atoms 1
Software Software Software Name Purpose XSCALE data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data scaling