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Crystal Structure of the apo-YsxC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 Sodium acetate, PEG 4000, Tris HCL, MnCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.12 42.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.67 α = 90 b = 36.52 β = 122.16 c = 83.253 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 IMAGE PLATE RIGAKU 2001-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 10 0.091 9.9 2.4 24474 24474
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) 2 2.05 93.4 0.392 2.2
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MIR THROUGHOUT 2 10 23172 1243 96.36 0.17717 0.17329 0.25084 RANDOM 17.422
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] -0.3 -0.74 0.07 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.599 r_scangle_it 4.242 r_dihedral_angle_1_deg 3.85 r_scbond_it 2.542 r_mcangle_it 1.522 r_angle_refined_deg 1.468 r_mcbond_it 0.829 r_xyhbond_nbd_refined 0.267 r_symmetry_hbond_refined 0.266 r_nbd_refined 0.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.599 r_scangle_it 4.242 r_dihedral_angle_1_deg 3.85 r_scbond_it 2.542 r_mcangle_it 1.522 r_angle_refined_deg 1.468 r_mcbond_it 0.829 r_xyhbond_nbd_refined 0.267 r_symmetry_hbond_refined 0.266 r_nbd_refined 0.253 r_symmetry_vdw_refined 0.233 r_chiral_restr 0.107 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_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 3040 Nucleic Acid Atoms Solvent Atoms 506 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling MLPHARE phasing