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Crystal structure of the c-type cytochrome SorU from Sinorhizobium meliloti
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PW9 pdb entry 4PW9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 1.8M TRI-SODIUM CITRATE PH 5.5, 0.1M GLYCINE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.48 50.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.949 α = 90 b = 129.327 β = 90 c = 197.059 γ = 90
Symmetry Space Group F 2 2 2
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 315r 2011-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.954 Australian Synchrotron MX2
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 2.19 50 99.9 0.133 6 4.1 23434
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 2.2 2.28 100 0.796 1.6 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT pdb entry 4PW9 2.19 39.19 23314 1201 98.6 0.188 0.185 0.1859 0.241 0.2433 RANDOM 32.84
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] 4.09 -1.64 -2.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.66 r_dihedral_angle_3_deg 15.129 r_dihedral_angle_4_deg 12.795 r_dihedral_angle_1_deg 5.739 r_scangle_it 2.406 r_scbond_it 1.46 r_angle_refined_deg 1.242 r_angle_other_deg 0.88 r_mcangle_it 0.874 r_mcbond_it 0.449
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.66 r_dihedral_angle_3_deg 15.129 r_dihedral_angle_4_deg 12.795 r_dihedral_angle_1_deg 5.739 r_scangle_it 2.406 r_scbond_it 1.46 r_angle_refined_deg 1.242 r_angle_other_deg 0.88 r_mcangle_it 0.874 r_mcbond_it 0.449 r_mcbond_other 0.099 r_chiral_restr 0.058 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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_mcangle_other r_scbond_other 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 2528 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 172
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling