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Structure of MsrB from Xanthomonas campestris (complex-like form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HCG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 7.5 293 18 % PEG 8000, 0.1M Na HEPES pH 7.5, 0.2M, 0.05M TRIS HCl pH 8 , microbatch under oil, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.67 53.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.436 α = 90 b = 74.203 β = 90 c = 122.941 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 CCD MAR CCD 165 mm 2005-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 1.24 EMBL/DESY, HAMBURG BW7A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.59 50 97.7 0.093 10.9 7.03 11793 11522
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 92 0.333 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 3HCG 2.59 24.25 11822 10912 543 97.18 0.215 0.19837 0.19588 0.1958 0.24737 0.2459 RANDOM 26.396
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] -0.44 0.36 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.509 r_dihedral_angle_3_deg 15.066 r_dihedral_angle_4_deg 14.468 r_dihedral_angle_1_deg 5.628 r_scangle_it 1.28 r_angle_refined_deg 1.137 r_scbond_it 0.728 r_mcangle_it 0.556 r_nbtor_refined 0.301 r_mcbond_it 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.509 r_dihedral_angle_3_deg 15.066 r_dihedral_angle_4_deg 14.468 r_dihedral_angle_1_deg 5.628 r_scangle_it 1.28 r_angle_refined_deg 1.137 r_scbond_it 0.728 r_mcangle_it 0.556 r_nbtor_refined 0.301 r_mcbond_it 0.298 r_symmetry_vdw_refined 0.252 r_nbd_refined 0.185 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.069 r_symmetry_hbond_refined 0.046 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 2350 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 17
Software Software Software Name Purpose DENZO data reduction MOLREP phasing REFMAC refinement SCALEPACK data scaling