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Crystal structure of a putative metal binding protein RUMGNA_00854 (ZP_02040092.1) from Ruminococcus gnavus ATCC 29149 at 1.30 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BB6 PDB entry 2BB6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.9 293 34.0% polyethylene glycol 400, 0.20M calcium acetate, 0.1M HEPES pH 7.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.83 32.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.685 α = 73.13 b = 30.474 β = 83.79 c = 47.156 γ = 89.3
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 MARMOSAIC 325 mm CCD double crystal monochromator 2011-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.3 29.504 95 0.067 7.9 2.5 36776 36776
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 1.3 1.33 92.2 0.589 0.589 1.2 2.5 2654
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 PDB entry 2BB6 1.3 29.504 36769 1824 95.03 0.1404 0.1379 0.1457 0.1887 0.1937 RANDOM 16.8017
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] 0.02 0.13 -0.09 0.06 -0.14 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.664 r_dihedral_angle_3_deg 11.339 r_sphericity_free 9.434 r_scangle_it 6.877 r_dihedral_angle_1_deg 5.936 r_scbond_it 4.807 r_sphericity_bonded 4.225 r_mcangle_it 3.902 r_mcbond_it 2.731 r_rigid_bond_restr 2.177
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.664 r_dihedral_angle_3_deg 11.339 r_sphericity_free 9.434 r_scangle_it 6.877 r_dihedral_angle_1_deg 5.936 r_scbond_it 4.807 r_sphericity_bonded 4.225 r_mcangle_it 3.902 r_mcbond_it 2.731 r_rigid_bond_restr 2.177 r_angle_refined_deg 1.714 r_mcbond_other 1.673 r_angle_other_deg 1.053 r_chiral_restr 0.106 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1504 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 44
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction MOLREP phasing SCALA data scaling REFMAC refinement MOSFLM data reduction