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Crystal structure of a ld-carboxypeptidase a (saro_1426) from novosphingobium aromaticivorans dsm at 1.89 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 NANODROP, 1.60M (NH4)2SO4, 0.1M Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.44 49.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.628 α = 90 b = 91.042 β = 90 c = 145.744 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 CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2008-12-07 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162, 0.97985, 0.97971 SSRL BL9-2
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 1.89 29.709 99.9 0.129 0.129 5.451 4.3 47086
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 1.89 1.95 100 0.845 0.845 0.9 3.6 3423
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 1.89 29.709 47036 2381 99.47 0.173 0.171 0.1743 0.207 0.209 RANDOM 27.268
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] 2.49 -0.21 -2.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.909 r_dihedral_angle_4_deg 17.205 r_dihedral_angle_3_deg 12.571 r_dihedral_angle_1_deg 6.014 r_scangle_it 1.727 r_mcangle_it 1.563 r_angle_refined_deg 1.492 r_scbond_it 1.311 r_mcbond_it 1.178 r_angle_other_deg 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.909 r_dihedral_angle_4_deg 17.205 r_dihedral_angle_3_deg 12.571 r_dihedral_angle_1_deg 6.014 r_scangle_it 1.727 r_mcangle_it 1.563 r_angle_refined_deg 1.492 r_scbond_it 1.311 r_mcbond_it 1.178 r_angle_other_deg 1 r_mcbond_other 0.32 r_symmetry_vdw_other 0.295 r_symmetry_hbond_refined 0.229 r_nbd_other 0.209 r_nbd_refined 0.208 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.168 r_symmetry_vdw_refined 0.161 r_chiral_restr 0.088 r_nbtor_other 0.087 r_bond_refined_d 0.017 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 4024 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 139
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 autoSHARP phasing SHELXD phasing