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Serratia marcescens short-chain dehydrogenase/reductase F98A/F202L
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZGW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7 298 50mM HEPES buffer (pH 7.0), 40% (v/v) tacsimate (pH 7.0), 2mM spermine, 2mM hexamine cobalt (III) chloride
Crystal Properties Matthews coefficient Solvent content 1.7 27.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.799 α = 90 b = 83.799 β = 90 c = 114.253 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 150 CCD RAYONIX MX300HE 2016-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) CC (Half) 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 1.87 67.58 99.5 0.051 0.053 0.014 0.991 44.7 13.7 34418
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 1.87 1.94
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 4ZGW 1.87 67.58 32399 1768 99.67 0.14918 0.14685 0.1599 0.19261 0.2027 RANDOM 20.61
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] -0.12 -0.12 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.611 r_dihedral_angle_4_deg 17.726 r_dihedral_angle_3_deg 13.239 r_long_range_B_refined 7.209 r_long_range_B_other 7.148 r_dihedral_angle_1_deg 6.423 r_scangle_other 6.006 r_scbond_it 3.946 r_scbond_other 3.945 r_mcangle_it 2.994
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.611 r_dihedral_angle_4_deg 17.726 r_dihedral_angle_3_deg 13.239 r_long_range_B_refined 7.209 r_long_range_B_other 7.148 r_dihedral_angle_1_deg 6.423 r_scangle_other 6.006 r_scbond_it 3.946 r_scbond_other 3.945 r_mcangle_it 2.994 r_mcangle_other 2.993 r_mcbond_it 2.129 r_mcbond_other 2.129 r_angle_refined_deg 2.029 r_angle_other_deg 1.101 r_chiral_restr 0.125 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3308 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling AMoRE phasing