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Crystal structure of Rib7 mutant D33N 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 10 % Tacsimate (pH 7.0), 10 % PEG 5000, and 100 mM HEPES (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 3.2 61.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.098 α = 90 b = 117.098 β = 90 c = 380.382 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 110 CCD ADSC QUANTUM 315r 2009-04-28 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 1.95 30 99.9 22.1 5.8 141352
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 1.95 2.02 100 0.652 5.8
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5XUX 1.95 30 134334 6953 99.75 0.24397 0.24167 0.28874 0.2723 RANDOM 44.209
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] -0.36 -0.18 -0.36 1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.167 r_dihedral_angle_3_deg 14.605 r_dihedral_angle_4_deg 13.079 r_long_range_B_refined 11.13 r_long_range_B_other 11.13 r_dihedral_angle_1_deg 6.864 r_scangle_other 4.423 r_mcangle_it 4.236 r_mcangle_other 4.236 r_scbond_it 2.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.167 r_dihedral_angle_3_deg 14.605 r_dihedral_angle_4_deg 13.079 r_long_range_B_refined 11.13 r_long_range_B_other 11.13 r_dihedral_angle_1_deg 6.864 r_scangle_other 4.423 r_mcangle_it 4.236 r_mcangle_other 4.236 r_scbond_it 2.747 r_scbond_other 2.747 r_mcbond_it 2.724 r_mcbond_other 2.724 r_angle_refined_deg 1.543 r_angle_other_deg 0.94 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 10403 Nucleic Acid Atoms Solvent Atoms 699 Heterogen Atoms 288
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing