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The structure of bd oxidase from Geobacillus thermodenitrificans
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 PEG 400, Ammonium sulfate, Na-HEPES
Crystal Properties Matthews coefficient Solvent content 4.39 71.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.06 α = 90 b = 120.86 β = 90 c = 122.72 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2014-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.738290 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) 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 3.8 49 99.6 0.096 0.014 21.2 32.1 16612
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.8 3.9 98.9 1.75 0.2 3.7 32.3
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 SAD THROUGHOUT 3.8 20 15690 807 98.91 0.30361 0.30261 0.3008 0.3252 0.3296 RANDOM 120.378
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] 20.23 13.78 -34.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.08 r_dihedral_angle_3_deg 11.842 r_dihedral_angle_4_deg 10.787 r_dihedral_angle_1_deg 6.282 r_angle_refined_deg 1.137 r_angle_other_deg 0.759 r_chiral_restr 0.052 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.08 r_dihedral_angle_3_deg 11.842 r_dihedral_angle_4_deg 10.787 r_dihedral_angle_1_deg 6.282 r_angle_refined_deg 1.137 r_angle_other_deg 0.759 r_chiral_restr 0.052 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 6343 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling SHELX phasing PHENIX phasing