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Crystal Structure of Burkholderia cenocepacia BcnB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WUB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 HEPES, PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.2 43.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.16 α = 90 b = 101.17 β = 97.2 c = 63.49 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 RAYONIX MX300HE 2015-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.6 37.33 97.3 0.061 0.997 11.3 3.8 82019
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 1.6 1.63 78.7 0.298 3.1 3495
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 1WUB 1.6 37.33 77882 4090 97.21 0.16189 0.16017 0.1707 0.19448 0.2018 RANDOM 22.251
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] -1.19 0.07 0.65 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.021 r_dihedral_angle_4_deg 14.176 r_dihedral_angle_3_deg 14.027 r_long_range_B_refined 7.044 r_long_range_B_other 7.032 r_dihedral_angle_1_deg 6.471 r_scangle_other 5.227 r_scbond_it 3.465 r_scbond_other 3.465 r_mcangle_it 2.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.021 r_dihedral_angle_4_deg 14.176 r_dihedral_angle_3_deg 14.027 r_long_range_B_refined 7.044 r_long_range_B_other 7.032 r_dihedral_angle_1_deg 6.471 r_scangle_other 5.227 r_scbond_it 3.465 r_scbond_other 3.465 r_mcangle_it 2.812 r_mcangle_other 2.812 r_angle_refined_deg 2.391 r_mcbond_it 1.86 r_mcbond_other 1.86 r_angle_other_deg 0.95 r_chiral_restr 0.143 r_bond_refined_d 0.024 r_gen_planes_refined 0.012 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5218 Nucleic Acid Atoms Solvent Atoms 482 Heterogen Atoms 203
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction