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Short-chain dehydrogenase/reductase from Serratia marcescens BCRC 10948
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V2G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 0.8 M sodium formate, 0.1 M sodium cacodylate, 25% w/v PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 1.71 27.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.871 α = 90 b = 83.871 β = 90 c = 115.057 γ = 90
Symmetry Space Group P 41 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 ADSC QUANTUM 315r 2014-10-18 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON OTHER 1.0
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 1.47 20 99.8 0.076 0.076 36.66 11.4 69956
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.52 100 4.44 11.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 3V2G 1.47 19.889 65062 3392 97.64 0.1674 0.16618 0.1761 0.19125 0.1963 RANDOM 18.231
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.303 r_dihedral_angle_4_deg 15.674 r_dihedral_angle_3_deg 14.105 r_scangle_it 7.153 r_dihedral_angle_1_deg 6.965 r_scbond_it 4.455 r_mcangle_it 2.977 r_angle_refined_deg 2.919 r_mcbond_it 1.788 r_chiral_restr 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.303 r_dihedral_angle_4_deg 15.674 r_dihedral_angle_3_deg 14.105 r_scangle_it 7.153 r_dihedral_angle_1_deg 6.965 r_scbond_it 4.455 r_mcangle_it 2.977 r_angle_refined_deg 2.919 r_mcbond_it 1.788 r_chiral_restr 0.314 r_bond_refined_d 0.035 r_gen_planes_refined 0.016 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3318 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data processing SCALEPACK data scaling MOLREP phasing Coot model building