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Crystal structure of Spr0440 glycoside hydrolase domain, Endo-D from Streptococcus pneumoniae R6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 289 20% w/v Polyethylene glycol 4000, 0.1M Sodium acetate trihydrate pH 4.6, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.704281 27.828815
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.14 α = 90 b = 59.06 β = 110.27 c = 94.89 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2008-12-06 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MAR CCD 165 mm 2008-01-18 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418 2 SYNCHROTRON BSRF BEAMLINE 3W1A 0.9790,0.9793,0.9700 BSRF 3W1A
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 1.86 24.66 97.1 0.066 0.078 14.7 3.4 57291 20.9
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) 1.86 1.98 88.4 0.406 0.482 3.1 3.3 7581
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 1.87 24.66 54391 2899 97.74 0.16352 0.16128 0.1601 0.20435 0.2023 RANDOM 21.169
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] -1.76 -1.16 -0.94 1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.744 r_dihedral_angle_4_deg 18.1 r_dihedral_angle_3_deg 14.761 r_dihedral_angle_1_deg 6.67 r_scangle_it 3.433 r_scbond_it 2.399 r_angle_refined_deg 1.389 r_mcangle_it 1.273 r_mcbond_it 0.95 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.744 r_dihedral_angle_4_deg 18.1 r_dihedral_angle_3_deg 14.761 r_dihedral_angle_1_deg 6.67 r_scangle_it 3.433 r_scbond_it 2.399 r_angle_refined_deg 1.389 r_mcangle_it 1.273 r_mcbond_it 0.95 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.218 r_nbd_refined 0.19 r_symmetry_hbond_refined 0.149 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 5068 Nucleic Acid Atoms Solvent Atoms 727 Heterogen Atoms 10
Software Software Software Name Purpose MAR345dtb data collection SOLVE phasing REFMAC refinement MOSFLM data reduction SCALEPACK data scaling