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Crystal structure of an ntf2-like protein with a cystatin-like fold (saro_3722) from novosphingobium aromaticivorans dsm at 1.16 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 NANODROP, 20.0% PEG 6000, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.56 51.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.135 α = 90 b = 63.135 β = 90 c = 75.118 γ = 120
Symmetry Space Group P 3 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 ADSC QUANTUM 315 2007-09-14 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.9797, 1.0000 ALS 8.2.1
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 1.16 27.338 99.5 0.085 0.085 5.6 4.7 60052 9.28
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 1.16 1.19 94.4 0.618 0.618 1.2 3.1 4170
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 1.16 27.338 60050 2995 99.39 0.142 0.141 0.1384 0.172 0.1681 RANDOM 9.74
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] -0.04 -0.02 -0.04 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.727 r_dihedral_angle_4_deg 19.099 r_dihedral_angle_3_deg 11.91 r_sphericity_free 11.749 r_scangle_it 6.922 r_dihedral_angle_1_deg 6.327 r_sphericity_bonded 5.333 r_scbond_it 5.209 r_mcangle_it 3.164 r_mcbond_it 2.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.727 r_dihedral_angle_4_deg 19.099 r_dihedral_angle_3_deg 11.91 r_sphericity_free 11.749 r_scangle_it 6.922 r_dihedral_angle_1_deg 6.327 r_sphericity_bonded 5.333 r_scbond_it 5.209 r_mcangle_it 3.164 r_mcbond_it 2.84 r_rigid_bond_restr 2.217 r_mcbond_other 1.812 r_angle_refined_deg 1.747 r_angle_other_deg 1.017 r_symmetry_vdw_other 0.344 r_nbd_refined 0.276 r_nbd_other 0.225 r_nbtor_refined 0.181 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.175 r_symmetry_vdw_refined 0.139 r_chiral_restr 0.103 r_nbtor_other 0.088 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1156 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction