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Crystal structure of type 2 PDF from Streptococcus agalactiae, crystallized in imidazole buffer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AIE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 7% PEG-8000 , 100mM Imidazole pH7.5, 300mM Zn Acetate
Crystal Properties Matthews coefficient Solvent content 2.62 53.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.32 α = 90 b = 65.55 β = 90 c = 88.71 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 2007-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9755 ESRF ID14-4
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 2 50 99.9 0.09 17.04 7.1 16886 2 2
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 2 2.12 99.3 0.295 6.63 7.1
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 2AIE 2 44.37 16041 845 100 0.16116 0.15871 0.1683 0.20774 0.2092 RANDOM 9.111
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] 0.4 0.52 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.66 r_dihedral_angle_4_deg 25.437 r_dihedral_angle_3_deg 13.303 r_dihedral_angle_1_deg 5.701 r_scangle_it 3.792 r_scbond_it 2.355 r_angle_refined_deg 1.557 r_mcangle_it 1.222 r_mcbond_it 0.818 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.66 r_dihedral_angle_4_deg 25.437 r_dihedral_angle_3_deg 13.303 r_dihedral_angle_1_deg 5.701 r_scangle_it 3.792 r_scbond_it 2.355 r_angle_refined_deg 1.557 r_mcangle_it 1.222 r_mcbond_it 0.818 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.251 r_xyhbond_nbd_refined 0.247 r_nbd_refined 0.2 r_metal_ion_refined 0.17 r_symmetry_hbond_refined 0.148 r_symmetry_metal_ion_refined 0.13 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other 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 1575 Nucleic Acid Atoms Solvent Atoms 325 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling FRODO model building PHASER phasing