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Structure of putative short-chain dehydrogenase (Saro_0793) from Novosphingobium aromaticivorans
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 2.4 M Sodium Malonate pH 7.5, Vapor diffusion, Sitting drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.31 46.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.683 α = 90 b = 100.753 β = 101.91 c = 63.463 γ = 90
Symmetry Space Group P 1 21 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 2009-04-25 SINGLE WAVELENGTH 2 1 x-ray CCD ADSC QUANTUM 315 2009-04-25
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.9793 NSLS X25 2 SYNCHROTRON NSLS BEAMLINE X29A 0.9793 NSLS X29A
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 1.9 50 99.7 0.091 13.3 7.2 49623
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) 1.9 1.97 99.1 0.475 6
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 1.9 50 47074 2522 98.76 0.20248 0.20082 0.1979 0.23346 0.2289 RANDOM 51.542
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] 2.26 -1.5 -0.91 -1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.503 r_dihedral_angle_4_deg 21.314 r_dihedral_angle_3_deg 16.247 r_dihedral_angle_1_deg 5.859 r_scangle_it 4.024 r_scbond_it 2.443 r_mcangle_it 1.614 r_angle_refined_deg 1.432 r_mcbond_it 0.9 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.503 r_dihedral_angle_4_deg 21.314 r_dihedral_angle_3_deg 16.247 r_dihedral_angle_1_deg 5.859 r_scangle_it 4.024 r_scbond_it 2.443 r_mcangle_it 1.614 r_angle_refined_deg 1.432 r_mcbond_it 0.9 r_chiral_restr 0.108 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4189 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction SHELXD phasing SHELXE model building CCP4 phasing