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Crystal structure of a proline dipeptidase from streptococcus pneumoniae tigr4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 Tris(0.1M, PH=8.5), LITHIUM SULFATE (0.2M, PH=N/A), AMMONIUM SULFATE (2M, PH=N/A), TEMPERATURE 277K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 5.03 75.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.073 α = 90 b = 118.073 β = 90 c = 185.348 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 ADSC QUANTUM 315 MIRROR 2009-05-31 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97940, 0.97937 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 99.58 100 0.091 0.091 38.209 9.9 168476 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.02 94.1 0.8 0.8 2.8 7.5
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 MAD THROUGHOUT 2 99.58 88411 4442 99.5 0.184 0.183 0.1906 0.204 0.2108 RANDOM 29.44
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] -0.35 -0.35 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.086 r_dihedral_angle_4_deg 16.888 r_dihedral_angle_3_deg 15.686 r_scangle_it 7.23 r_dihedral_angle_1_deg 6.516 r_scbond_it 4.569 r_mcangle_it 3.242 r_angle_refined_deg 2.493 r_mcbond_it 1.884 r_chiral_restr 0.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.086 r_dihedral_angle_4_deg 16.888 r_dihedral_angle_3_deg 15.686 r_scangle_it 7.23 r_dihedral_angle_1_deg 6.516 r_scbond_it 4.569 r_mcangle_it 3.242 r_angle_refined_deg 2.493 r_mcbond_it 1.884 r_chiral_restr 0.228 r_bond_refined_d 0.037 r_gen_planes_refined 0.014 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4440 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 20
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 phasing MLPHARE phasing DM model building SHELXD phasing RESOLVE model building ARP/wARP model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling DM phasing RESOLVE phasing