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Crystal structure of a thioesterase superfamily protein (cc_3309) from caulobacter vibrioides at 1.85 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 6.6 277 0.2M NH4Formate, 20.0% PEG-3350, No Buffer, pH 6.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K 2 VAPOR DIFFUSION, SITTING DROP, NANODROP 4.2 277 40.0% PEG-300, 0.1M Phosphate Citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.44 α = 90 b = 53.44 β = 90 c = 99.09 γ = 90
Symmetry Space Group P 42 21 2
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 2006-05-14 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD ADSC QUANTUM 315 Flat mirror (vertical focusing) 2006-05-08 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2 2 SYNCHROTRON SSRL BEAMLINE BL11-1 0.979008, 0.979318, 0.918370 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 1.85 50 99.8 0.073 13.7 6.8 12896
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 1.85 1.9 100 0.805 5.5 887
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 1.85 28.1 12846 628 99.76 0.21 0.208 0.2129 0.244 0.2425 RANDOM 36.857
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 -1.75 3.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.09 r_dihedral_angle_4_deg 18.817 r_dihedral_angle_3_deg 14.465 r_dihedral_angle_1_deg 6.901 r_scangle_it 4.12 r_scbond_it 3.382 r_mcangle_it 2.338 r_mcbond_it 1.598 r_angle_refined_deg 1.56 r_angle_other_deg 0.823
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.09 r_dihedral_angle_4_deg 18.817 r_dihedral_angle_3_deg 14.465 r_dihedral_angle_1_deg 6.901 r_scangle_it 4.12 r_scbond_it 3.382 r_mcangle_it 2.338 r_mcbond_it 1.598 r_angle_refined_deg 1.56 r_angle_other_deg 0.823 r_mcbond_other 0.297 r_nbd_refined 0.223 r_nbd_other 0.203 r_symmetry_vdw_other 0.192 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.143 r_symmetry_hbond_refined 0.128 r_symmetry_vdw_refined 0.126 r_nbtor_other 0.085 r_chiral_restr 0.084 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1089 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 31
Software Software Software Name Purpose MolProbity model building REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction