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Crystal structure of the hydrogenase assembly chaperone HypC/HupF family protein from Shewanella oneidensis MR-1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 20% PEG 3350, 0.2M Ammonium citrate, 0.3M NDSB211, 0.5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.01 38.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.864 α = 90 b = 58.316 β = 127.89 c = 51.924 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 315 Mirrors 2008-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97921 APS 19-ID
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 1.85 38.75 98.6 0.102 10.1 4.5 15804 15804 30.17
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 1.85 1.88 100 0.328 3.92 4.5 817
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 (All) 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 1.85 38.75 14966 14966 789 98.62 0.203 0.203 0.202 0.2003 0.234 0.2332 RANDOM 36.876
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 0.45 -1.05 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.523 r_dihedral_angle_4_deg 24.768 r_dihedral_angle_3_deg 15.484 r_scangle_it 5.962 r_dihedral_angle_1_deg 5.783 r_scbond_it 3.683 r_mcangle_it 2.248 r_angle_refined_deg 1.851 r_mcbond_it 1.611 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.523 r_dihedral_angle_4_deg 24.768 r_dihedral_angle_3_deg 15.484 r_scangle_it 5.962 r_dihedral_angle_1_deg 5.783 r_scbond_it 3.683 r_mcangle_it 2.248 r_angle_refined_deg 1.851 r_mcbond_it 1.611 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.299 r_symmetry_hbond_refined 0.257 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.139 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 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_refined 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1285 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing MLPHARE phasing DM phasing SHELXD phasing RESOLVE phasing Coot model building