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Structure of the hypothetical oxidoreductase YcnD from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BKJ PDB ENTRY 1BKJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 PEG-400, CaCl2, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.101 α = 90 b = 89.075 β = 90 c = 93.608 γ = 90
Symmetry Space Group C 2 2 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 MARRESEARCH 2004-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8126 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 18 99.6 0.045 47 7 21381 21381 15.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 95.9 0.202 8.1 1345
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 PDB ENTRY 1BKJ 1.85 17.79 21381 21381 1076 99.6 0.171 0.171 0.1751 0.197 0.1765 RANDOM 19.5
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] 2.58 -2.06 -0.53
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21 c_scangle_it 3.05 c_scbond_it 1.97 c_mcangle_it 1.78 c_mcbond_it 1.19 c_angle_deg 1.1 c_improper_angle_d 0.78 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1961 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 33
Software Software Software Name Purpose CNS refinement MAR345 data collection SCALEPACK data scaling EPMR phasing