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Crystal structure of a putative molybdenum cofactor biosynthesis protein F from Burkholderia cenocepacia J2315
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 0.2 M Calcium Chloride, 0.1 M Tris-HCl, 25 % (w/v) PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 1.96 37.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.402 α = 90 b = 46.163 β = 99.14 c = 77.293 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 MARMOSAIC 225 mm CCD Beryllium Lenses 2014-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.9 30 96.7 0.08 24.8 6.6 37347 37347 -3 27.3
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 1.9 1.93 93.7 0.5 4.2 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 1.9 29.57 35312 35312 1869 95.87 0.16274 0.16028 0.1721 0.20871 0.218 RANDOM 21.182
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] -0.19 0.01 0.07 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.17 r_dihedral_angle_4_deg 15.509 r_dihedral_angle_3_deg 13.449 r_dihedral_angle_1_deg 6.338 r_long_range_B_refined 6.009 r_long_range_B_other 5.801 r_scangle_other 3.391 r_scbond_it 2.139 r_scbond_other 2.138 r_mcangle_it 1.839
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.17 r_dihedral_angle_4_deg 15.509 r_dihedral_angle_3_deg 13.449 r_dihedral_angle_1_deg 6.338 r_long_range_B_refined 6.009 r_long_range_B_other 5.801 r_scangle_other 3.391 r_scbond_it 2.139 r_scbond_other 2.138 r_mcangle_it 1.839 r_mcangle_other 1.839 r_angle_refined_deg 1.789 r_mcbond_it 1.198 r_mcbond_other 1.197 r_angle_other_deg 0.841 r_chiral_restr 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 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 4113 Nucleic Acid Atoms Solvent Atoms 474 Heterogen Atoms 2
Software Software Software Name Purpose Blu-Ice data collection PHENIX model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing