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Hybrid Cluster Protein from Desulfovibrio vulgaris. X-ray structure at 1.25A resolution using synchrotron radiation.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E2U PDB FROM ENTRY 1E2U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.9 293 25-30% PEG 8000 0.1M MES PH 5.9, 0.2M MAGNESIUM ACETATE, T=277K
Crystal Properties Matthews coefficient Solvent content 2.61 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.81 α = 90 b = 64.53 β = 90 c = 151.87 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 IMAGE PLATE MARRESEARCH PLATINUM COATED FUSED QUARTZ MIRROR 1999-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 SRS PX9.6
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 1.25 19.92 94.6 0.063 6.2 2.4 163543
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 1.25 1.34 86.4 0.331 1.6 1.7
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB FROM ENTRY 1E2U 1.25 19.92 155271 8216 94.6 0.158 0.157 0.1686 0.173 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.064 r_scbond_it 1.895 r_angle_other_deg 1.467 r_mcangle_it 1.217 r_dihedral_angle_3_deg 1.168 r_mcbond_it 0.693 r_symmetry_hbond_refined 0.366 r_nbtor_other 0.339 r_symmetry_vdw_refined 0.277 r_nbd_refined 0.231
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.064 r_scbond_it 1.895 r_angle_other_deg 1.467 r_mcangle_it 1.217 r_dihedral_angle_3_deg 1.168 r_mcbond_it 0.693 r_symmetry_hbond_refined 0.366 r_nbtor_other 0.339 r_symmetry_vdw_refined 0.277 r_nbd_refined 0.231 r_symmetry_vdw_other 0.217 r_xyhbond_nbd_refined 0.197 r_nbd_other 0.18 r_chiral_restr 0.106 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_angle_refined_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_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 4217 Nucleic Acid Atoms Solvent Atoms 1015 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing