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Crystal Structure of Geobacillus thermodenitrificans EssB extracellular fragment
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 3 M MALONATE PH7.0, 10 MM ZNCL2
Crystal Properties Matthews coefficient Solvent content 4.56 72.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.89 α = 90 b = 110.62 β = 103.34 c = 97.41 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 CCD ADSC QUANTUM 315r MIRRORS 2010-07-28 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 2.4 29.46 97.4 0.07 11.7 4.6 52114 56.6
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 2.4 2.53 96.3 0.44 3 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT NONE 2.4 94.782 1 52094 2642 97.145 0.188 0.1862 0.183 0.2215 0.2187 60.064
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] -0.188 -1.366 -0.335 -0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.311 r_dihedral_angle_4_deg 17.626 r_dihedral_angle_3_deg 16.875 r_dihedral_angle_1_deg 4.768 r_scangle_it 3.113 r_scbond_it 1.842 r_angle_refined_deg 1.202 r_mcangle_it 1.134 r_mcbond_it 0.565 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.311 r_dihedral_angle_4_deg 17.626 r_dihedral_angle_3_deg 16.875 r_dihedral_angle_1_deg 4.768 r_scangle_it 3.113 r_scbond_it 1.842 r_angle_refined_deg 1.202 r_mcangle_it 1.134 r_mcbond_it 0.565 r_nbtor_refined 0.305 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.194 r_symmetry_hbond_refined 0.186 r_xyhbond_nbd_refined 0.158 r_metal_ion_refined 0.119 r_chiral_restr 0.083 r_bond_refined_d 0.011 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_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 5000 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing