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Structure of a GTP Pyrophosphokinase Family Protein from Streptococcus pneumoniae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 50mg/ml protein, 0.2M Na Malonate, 20% PEG3350, 25% Glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.55 51.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.843 α = 90 b = 104.843 β = 90 c = 170.562 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 CCD MARMOSAIC 300 mm CCD 2005-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97857 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 38 99.53 21127 21127
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.462 97.64
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.4 38 21127 21127 1130 99.53 0.18487 0.18487 0.18219 0.23423 0.3002 RANDOM 73.262
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] -1.23 -0.61 -1.23 1.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.104 r_dihedral_angle_3_deg 19.104 r_dihedral_angle_4_deg 16.687 r_dihedral_angle_1_deg 6.307 r_scangle_it 4.066 r_scbond_it 2.631 r_mcangle_it 1.571 r_angle_refined_deg 1.464 r_mcbond_it 1.028 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.104 r_dihedral_angle_3_deg 19.104 r_dihedral_angle_4_deg 16.687 r_dihedral_angle_1_deg 6.307 r_scangle_it 4.066 r_scbond_it 2.631 r_mcangle_it 1.571 r_angle_refined_deg 1.464 r_mcbond_it 1.028 r_nbtor_refined 0.305 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.21 r_xyhbond_nbd_refined 0.188 r_symmetry_hbond_refined 0.164 r_chiral_restr 0.116 r_bond_refined_d 0.015 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_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3259 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data scaling HKL-3000 phasing SHELXD phasing MLPHARE phasing DM phasing CCP4 phasing RESOLVE phasing Coot model building O model building ARP/wARP model building