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Crystal structure of a cystatin-like protein (RUMGNA_02398) from Ruminococcus gnavus ATCC 29149 at 2.10 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M magnesium formate, 20.0% polyethylene glycol 3350, The additive is 0.1 M Cesium Chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.14 42.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.394 α = 90 b = 109.013 β = 90 c = 137.307 γ = 90
Symmetry Space Group P 21 21 21
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 DECTRIS PILATUS 6M Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2014-03-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.9798,0.97917 SSRL BL11-1
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 2.1 29.671 96.2 0.085 11 45198 -3 35.714
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 2.1 2.17 93.5 0.829 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.1 29.671 45054 2271 98.05 0.1937 0.1913 0.1969 0.2404 0.2464 RANDOM 50.8766
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] -1.75 -2.56 4.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.167 r_dihedral_angle_4_deg 17.482 r_dihedral_angle_3_deg 14.852 r_dihedral_angle_1_deg 5.964 r_mcangle_it 3.872 r_mcbond_it 2.61 r_mcbond_other 2.608 r_angle_refined_deg 1.224 r_angle_other_deg 0.698 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.167 r_dihedral_angle_4_deg 17.482 r_dihedral_angle_3_deg 14.852 r_dihedral_angle_1_deg 5.964 r_mcangle_it 3.872 r_mcbond_it 2.61 r_mcbond_other 2.608 r_angle_refined_deg 1.224 r_angle_other_deg 0.698 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5993 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 1
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing XSCALE data scaling REFMAC refinement XDS data reduction SHELXD phasing