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Crystal structure of Rib7 mutant D33A from Methanosarcina mazei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XUX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 20-25 % Tacsimate (pH 7.0), 2 % PEG 3350, and 100 mM HEPES (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 2.96 58.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.147 α = 90 b = 70.147 β = 90 c = 217.458 γ = 120
Symmetry Space Group P 64 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315r 2008-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 20 99.9 65.9 20.7 22298
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 2.07 100 0.744 4.9 20
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 5XUX 2 19.907 21144 1053 99.52 0.23579 0.23495 0.2409 0.25172 0.2606 RANDOM 50.384
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] 0.93 0.46 0.93 -3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.981 r_dihedral_angle_4_deg 17.56 r_dihedral_angle_3_deg 13.199 r_long_range_B_refined 8.503 r_long_range_B_other 8.501 r_scangle_other 5.68 r_dihedral_angle_1_deg 5.679 r_mcangle_it 3.925 r_mcangle_other 3.925 r_scbond_it 3.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.981 r_dihedral_angle_4_deg 17.56 r_dihedral_angle_3_deg 13.199 r_long_range_B_refined 8.503 r_long_range_B_other 8.501 r_scangle_other 5.68 r_dihedral_angle_1_deg 5.679 r_mcangle_it 3.925 r_mcangle_other 3.925 r_scbond_it 3.71 r_scbond_other 3.708 r_mcbond_it 2.889 r_mcbond_other 2.881 r_angle_refined_deg 1.585 r_angle_other_deg 0.937 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1687 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing