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Crystal structure of Rib7 from Methanosarcina mazei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AZN
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 3.24 62.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.457 α = 90 b = 118.457 β = 90 c = 375.551 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 2008-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 1.0 NSRRC BL13C1
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 2.27 50 99.9 18.9 5.5 90715
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 2.27 2.35 99.9 0.688 4.7
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 2AZN 2.27 50 86239 4451 99.7 0.19958 0.19806 0.22825 0.2432 RANDOM 50.612
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] 0.16 0.08 0.16 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.914 r_dihedral_angle_3_deg 13.915 r_dihedral_angle_4_deg 13.195 r_long_range_B_refined 7.46 r_long_range_B_other 7.45 r_dihedral_angle_1_deg 6.613 r_scangle_other 4.678 r_mcangle_it 3.77 r_mcangle_other 3.769 r_scbond_it 2.824
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.914 r_dihedral_angle_3_deg 13.915 r_dihedral_angle_4_deg 13.195 r_long_range_B_refined 7.46 r_long_range_B_other 7.45 r_dihedral_angle_1_deg 6.613 r_scangle_other 4.678 r_mcangle_it 3.77 r_mcangle_other 3.769 r_scbond_it 2.824 r_scbond_other 2.824 r_mcbond_it 2.384 r_mcbond_other 2.384 r_angle_refined_deg 1.398 r_angle_other_deg 0.888 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 10388 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms 288
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing