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The crystal structure of MalX from Streptococcus pneumoniae in complex with maltopentaose.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GHA PDB ENTRY 2GHA
Crystallization Crystal Properties Matthews coefficient Solvent content 2.53 51.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.37 α = 90 b = 127.88 β = 90 c = 51.99 γ = 90
Symmetry Space Group P 21 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 113 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 20 92.7 0.06 17.3 4.3 29101 2
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 2.05 94.1 0.31 3.5 4.1
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 PDB ENTRY 2GHA 2 20 27619 1482 92.23 0.2089 0.20653 0.2051 0.25063 0.25 RANDOM 31.078
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] 3.35 -1.23 -2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.878 r_dihedral_angle_4_deg 22.882 r_dihedral_angle_3_deg 17.769 r_dihedral_angle_1_deg 6.651 r_scangle_it 2.431 r_scbond_it 1.549 r_angle_refined_deg 1.267 r_mcangle_it 1.146 r_mcbond_it 0.646 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.878 r_dihedral_angle_4_deg 22.882 r_dihedral_angle_3_deg 17.769 r_dihedral_angle_1_deg 6.651 r_scangle_it 2.431 r_scbond_it 1.549 r_angle_refined_deg 1.267 r_mcangle_it 1.146 r_mcbond_it 0.646 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.273 r_symmetry_hbond_refined 0.23 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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_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 2852 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement PHASER phasing