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Crystal structure of a cystatin-like protein (saro_2766) from novosphingobium aromaticivorans dsm at 1.40 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 2.0000M (NH4)2SO4, 2.0000% PEG-400, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.08 40.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.54 α = 90 b = 79.54 β = 90 c = 79.54 γ = 90
Symmetry Space Group P 21 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 Flat collimating mirror, toroid focusing mirror 2008-08-10 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97929 SSRL BL9-2
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 1.4 28.127 99.3 0.048 13.99 33205 -3 13.35
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) 1.4 1.45 97 0.55 2
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 1.4 28.127 33165 1672 99.87 0.143 0.142 0.1498 0.161 0.1651 RANDOM 16.11
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.973 r_dihedral_angle_4_deg 17.2 r_dihedral_angle_3_deg 11.86 r_dihedral_angle_1_deg 6.624 r_sphericity_free 6.287 r_sphericity_bonded 3.057 r_scangle_it 2.888 r_mcangle_it 2.606 r_scbond_it 2.131 r_mcbond_it 1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.973 r_dihedral_angle_4_deg 17.2 r_dihedral_angle_3_deg 11.86 r_dihedral_angle_1_deg 6.624 r_sphericity_free 6.287 r_sphericity_bonded 3.057 r_scangle_it 2.888 r_mcangle_it 2.606 r_scbond_it 2.131 r_mcbond_it 1.99 r_angle_refined_deg 1.545 r_rigid_bond_restr 1.363 r_angle_other_deg 0.971 r_mcbond_other 0.859 r_symmetry_vdw_other 0.295 r_nbd_refined 0.223 r_nbd_other 0.214 r_symmetry_vdw_refined 0.186 r_nbtor_refined 0.172 r_symmetry_hbond_refined 0.169 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.112 r_nbtor_other 0.086 r_bond_refined_d 0.015 r_bond_other_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1203 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHARP phasing