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Hexameric ring of Methanococcus voltae RadA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T4G PDB entry 1T4G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 294 33% PEG 400, 1.0 M NaNO3, 0.05 M MES-NaOH Buffer at pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.97 58.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.351 α = 90 b = 118.577 β = 138.05 c = 141.731 γ = 90
Symmetry Space Group C 1 2 1
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 Brukers Proteum 2009-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE Cu FINE FOCUS 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.6 30 90.5 0.07 0.07 8.5 3.6 63397 57374 55
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 90.1 0.293 0.293 2.6 3.1 6401
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1T4G 2.6 30 63397 54446 2928 90.11 0.20916 0.20916 0.20599 0.2032 0.26584 0.2627 RANDOM 55.71
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] -3.91 -1.72 2.55 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.438 r_dihedral_angle_4_deg 21.157 r_dihedral_angle_3_deg 20.634 r_dihedral_angle_1_deg 6.113 r_angle_refined_deg 1.7 r_chiral_restr 0.111 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.438 r_dihedral_angle_4_deg 21.157 r_dihedral_angle_3_deg 20.634 r_dihedral_angle_1_deg 6.113 r_angle_refined_deg 1.7 r_chiral_restr 0.111 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11982 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 48
Software Software Software Name Purpose PROTEUM PLUS data collection PHASER phasing REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling