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Dodecahedral assembly of MhpD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SV6 PDB ENTRY 1SV6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 3.2 1M NA/K PHOSPHATE PH3.2
Crystal Properties Matthews coefficient Solvent content 3.76 67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 207.35 α = 90 b = 207.35 β = 90 c = 545.471 γ = 120
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 2007-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.8 36.4 97.9 0.14 6.7 2.2 210704 45.8
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 2.8 2.95 95.7 0.53 1.8 2.1
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 1SV6 2.8 35.26 200121 10564 97.88 0.22253 0.22194 0.2195 0.23382 0.2312 RANDOM 35.637
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_dihedral_angle_2_deg 36.06 r_dihedral_angle_3_deg 21.23 r_dihedral_angle_4_deg 20.025 r_dihedral_angle_1_deg 5.887 r_scangle_it 4.083 r_scbond_it 2.269 r_mcangle_it 1.359 r_angle_refined_deg 1.313 r_mcbond_it 0.629 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.06 r_dihedral_angle_3_deg 21.23 r_dihedral_angle_4_deg 20.025 r_dihedral_angle_1_deg 5.887 r_scangle_it 4.083 r_scbond_it 2.269 r_mcangle_it 1.359 r_angle_refined_deg 1.313 r_mcbond_it 0.629 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_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 39720 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 230
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing