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Structure of CbpJ from Streptococcus Pneumoniae TIGR4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V04
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 10% PEG 20K, 0.1 M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.77 55.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.523 α = 90 b = 77.378 β = 90 c = 187.848 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 MARRESEARCH 2010-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97923 SSRF BL17U
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 50 93.4 0.072 10.259 6.6 51107
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 2.07 0.199
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 2V04 2 48.68 48373 2591 93.3 0.21603 0.21389 0.2165 0.25603 0.2556 RANDOM 42.374
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] 4.31 -0.82 -3.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.331 r_dihedral_angle_4_deg 17.856 r_dihedral_angle_3_deg 14.925 r_dihedral_angle_1_deg 5.964 r_scangle_it 3.337 r_scbond_it 2.131 r_mcangle_it 1.771 r_angle_refined_deg 1.289 r_mcbond_it 0.959 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.331 r_dihedral_angle_4_deg 17.856 r_dihedral_angle_3_deg 14.925 r_dihedral_angle_1_deg 5.964 r_scangle_it 3.337 r_scbond_it 2.131 r_mcangle_it 1.771 r_angle_refined_deg 1.289 r_mcbond_it 0.959 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4909 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing