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Crystal structure of a protein of unknown function with a cystatin-like fold (saro_2880) from novosphingobium aromaticivorans dsm at 1.30 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 277 NANODROP, 0.020M CaCl2, 30.0% MPD, 0.1M Acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.36 47.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.343 α = 90 b = 54.343 β = 90 c = 93.947 γ = 120
Symmetry Space Group P 32 2 1
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 Flat mirror (vertical focusing) 2008-11-15 M SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97821 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 26.1 98.3 0.066 0.066 6.15 6.2 39549
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 81.9 0.442 0.442 1.8 4 2374
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 SAD THROUGHOUT 1.3 26.1 39502 1969 98.25 0.121 0.12 0.1141 0.143 0.1344 RANDOM 17.837
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] 0.07 0.04 0.07 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.566 r_sphericity_free 13.334 r_dihedral_angle_3_deg 11.132 r_dihedral_angle_1_deg 6.688 r_scangle_it 6.571 r_dihedral_angle_4_deg 6.511 r_sphericity_bonded 6.458 r_scbond_it 4.845 r_mcangle_it 4.112 r_mcbond_it 3.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.566 r_sphericity_free 13.334 r_dihedral_angle_3_deg 11.132 r_dihedral_angle_1_deg 6.688 r_scangle_it 6.571 r_dihedral_angle_4_deg 6.511 r_sphericity_bonded 6.458 r_scbond_it 4.845 r_mcangle_it 4.112 r_mcbond_it 3.081 r_mcbond_other 2.508 r_rigid_bond_restr 2.373 r_angle_refined_deg 1.807 r_angle_other_deg 0.999 r_chiral_restr 0.112 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1009 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXD phasing autoSHARP phasing