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Crystal structure of the cold shock domain protein from Neisseria meningitidis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.7 293 0.8 M Sodium dihydrogen phosphate, 1.2 M di-potassium hydrogen phosphate, 100 mM Acetate pH 4.5, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.7 54.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.369 α = 90 b = 59.369 β = 90 c = 89.423 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 MARMOSAIC 225 mm CCD 2006-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97900 ESRF BM14
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 2.6 30 98.5 0.127 29.2 23.9 5271 -1.5
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 2.6 2.69 88.8 0.834 1.7 13.1 459
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 SAD THROUGHOUT 2.6 30 4951 270 98.4 0.23646 0.23312 0.243 0.29663 0.2048 RANDOM 61.159
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] -3.46 -3.46 6.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.476 r_dihedral_angle_3_deg 17.822 r_dihedral_angle_4_deg 15.191 r_scangle_it 9.741 r_scbond_it 7.333 r_mcangle_it 5.603 r_dihedral_angle_1_deg 5.359 r_mcbond_it 4.278 r_mcbond_other 1.167 r_angle_refined_deg 1.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.476 r_dihedral_angle_3_deg 17.822 r_dihedral_angle_4_deg 15.191 r_scangle_it 9.741 r_scbond_it 7.333 r_mcangle_it 5.603 r_dihedral_angle_1_deg 5.359 r_mcbond_it 4.278 r_mcbond_other 1.167 r_angle_refined_deg 1.022 r_angle_other_deg 0.793 r_symmetry_hbond_refined 0.208 r_nbd_refined 0.184 r_nbtor_refined 0.183 r_symmetry_vdw_other 0.173 r_nbd_other 0.17 r_symmetry_vdw_refined 0.166 r_xyhbond_nbd_refined 0.137 r_nbtor_other 0.084 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1014 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction SCALEPACK data scaling SHELXCD phasing SHELXE model building