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Hybrid Cluster Protein from Desulfovibrio desulfuricans X-ray structure at 1.25A resolution using synchrotron radiation at a wavelength of 0.933A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GN9 PDB FROM ENTRY 1GN9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 277 25% PEG 4000, 0.1M MES PH6.0, T=277K, pH 6.00
Crystal Properties Matthews coefficient Solvent content 2.03 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.33 α = 82.77 b = 61.65 β = 73.67 c = 72.25 γ = 87.31
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 CCD TOROIDAL MIRROR 2001-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 28.63 94.9 0.054 8 3.7 247243
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 1.29 85.3 0.215 3.1 3.7
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB FROM ENTRY 1GN9 1.25 28.63 234815 12427 94.9 0.13 0.129 0.145 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 2.731 r_scbond_it 1.731 r_angle_other_deg 1.536 r_dihedral_angle_3_deg 1.475 r_mcangle_it 1.102 r_nbtor_other 0.619 r_mcbond_it 0.615 r_symmetry_hbond_refined 0.34 r_symmetry_vdw_refined 0.328 r_nbd_refined 0.237
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.731 r_scbond_it 1.731 r_angle_other_deg 1.536 r_dihedral_angle_3_deg 1.475 r_mcangle_it 1.102 r_nbtor_other 0.619 r_mcbond_it 0.615 r_symmetry_hbond_refined 0.34 r_symmetry_vdw_refined 0.328 r_nbd_refined 0.237 r_xyhbond_nbd_refined 0.208 r_symmetry_vdw_other 0.206 r_nbd_other 0.191 r_chiral_restr 0.105 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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 8222 Nucleic Acid Atoms Solvent Atoms 1562 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALA data scaling AMoRE phasing