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Crystal Structure of Yvgn and cofactor NADPH from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B3E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 289 0.4M SODIUM NITRATE, 40% PEG3350, pH 7.5, Vapor diffusion, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.25 45.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.517 α = 90 b = 123.285 β = 90 c = 57.226 γ = 90
Symmetry Space Group P 21 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 SMART6000 2007-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 2.3 67.4 89 0.1 0.11 5.26 14 26027 23334 22.3
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 2.3 2.47 89 0.1 0.11 5.26 14.8 23334
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) 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 3B3E 2.4 20 2 26027 20421 1065 93.75 0.24007 0.23649 0.2424 0.30615 0.3061 RANDOM 9.578
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] 2.2 -3.37 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.338 r_dihedral_angle_4_deg 23.101 r_dihedral_angle_3_deg 20.11 r_dihedral_angle_1_deg 8.207 r_scangle_it 2.963 r_angle_refined_deg 1.992 r_scbond_it 1.983 r_mcangle_it 1.166 r_mcbond_it 0.716 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.338 r_dihedral_angle_4_deg 23.101 r_dihedral_angle_3_deg 20.11 r_dihedral_angle_1_deg 8.207 r_scangle_it 2.963 r_angle_refined_deg 1.992 r_scbond_it 1.983 r_mcangle_it 1.166 r_mcbond_it 0.716 r_nbtor_refined 0.31 r_symmetry_hbond_refined 0.27 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.157 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4452 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 96
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction PROTEUM PLUS data collection SAINT data reduction PROTEUM data scaling