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Guanylylpyridinol (GP)- and ATP-bound HcgE from Methanothermobacter marburgensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZUD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 35%(w/v)pentaerythritol ethoxylate 270, 200mM ammonium sulfate, 100mM sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature Room temperatureK
Crystal Properties Matthews coefficient Solvent content 2.65 53.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85 α = 90 b = 85 β = 90 c = 120.78 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 PIXEL PSI PILATUS 6M 2013-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.008 SLS X10SA
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 2.75 50 100 0.105 15 7.79 25386 -3
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 2.75 2.85 100 0.87 2.47
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 1ZUD 2.75 46.69 24213 1173 99.95 0.16759 0.16538 0.1655 0.21389 0.2133 RANDOM 60.84
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] 0.21 0.1 0.21 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.637 r_dihedral_angle_4_deg 23.024 r_dihedral_angle_3_deg 18.384 r_dihedral_angle_1_deg 8.522 r_mcangle_it 6.192 r_scbond_it 4.523 r_mcbond_it 3.975 r_angle_refined_deg 2.499 r_chiral_restr 0.15 r_bond_refined_d 0.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.637 r_dihedral_angle_4_deg 23.024 r_dihedral_angle_3_deg 18.384 r_dihedral_angle_1_deg 8.522 r_mcangle_it 6.192 r_scbond_it 4.523 r_mcbond_it 3.975 r_angle_refined_deg 2.499 r_chiral_restr 0.15 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 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_it 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 6220 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 280
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction MOLREP phasing