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The Structure of GlcB from Mycobacterium leprae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N8I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 MyleA18344aA1 PW34800 19.28mg/ml, 100mM HEPES pH7.5, 20%w/v PEG4000, 10% Isopropanol. Cryoprotection 20% ethylene glycol. , VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.3 46.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.61 α = 90 b = 59.74 β = 100.97 c = 118.46 γ = 90
Symmetry Space Group P 1 21 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 CCD RIGAKU SATURN 944+ 2012-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.1 50 99.7 0.1 12.24 85731 -3
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 2.1 2.15 99.1 0.43 3.17
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 1N8I 2.1 50 81426 4292 99.7 0.18341 0.18078 0.1851 0.23423 0.2368 RANDOM 23.128
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] -1.13 0.05 0.04 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.231 r_dihedral_angle_4_deg 19.913 r_dihedral_angle_3_deg 13.535 r_dihedral_angle_1_deg 6.326 r_angle_refined_deg 1.539 r_angle_other_deg 0.955 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.231 r_dihedral_angle_4_deg 19.913 r_dihedral_angle_3_deg 13.535 r_dihedral_angle_1_deg 6.326 r_angle_refined_deg 1.539 r_angle_other_deg 0.955 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10599 Nucleic Acid Atoms Solvent Atoms 866 Heterogen Atoms 10
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction