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Myrosinase from Sinapis alba with bound gluco-hydroximolactam and sulfate or ascorbate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E4M PDB ENTRY 1E4M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 HANGING DROP METHOD, 12 MG/ML PROTEIN IN 30 MM HEPES, PH 6.5, 0.05 % NAN3 PRECIPITANT 66 % SAT. AMMONIUM SULFATE, 100MM TRIS-HCL PH 7.0
Crystal Properties Matthews coefficient Solvent content 3.2 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.3 α = 90 b = 137.2 β = 90 c = 80.6 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 BENT MULTILAYER, SAGITALLY FOCUSING CRYSTAL 1998-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 1.6 37.3 99.7 0.076 0.076 5.2 4.2 110239
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 1.6 1.66 99.7 0.256 0.256 2 3.3
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-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1E4M 1.6 10 95835 4890 97.5 0.129 0.157 0.1591 RANDOM 20.5
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]
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 26.3 p_staggered_tor 11.7 p_planar_tor 8.2 p_scangle_it 3.8 p_mcangle_it 2.9 p_scbond_it 2.9 p_mcbond_it 2.2 p_multtor_nbd 0.305 p_singtor_nbd 0.17 p_xyhbond_nbd 0.161
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 26.3 p_staggered_tor 11.7 p_planar_tor 8.2 p_scangle_it 3.8 p_mcangle_it 2.9 p_scbond_it 2.9 p_mcbond_it 2.2 p_multtor_nbd 0.305 p_singtor_nbd 0.17 p_xyhbond_nbd 0.161 p_chiral_restr 0.126 p_planar_d 0.043 p_angle_d 0.032 p_plane_restr 0.027 p_bond_d 0.019 p_angle_deg p_hb_or_metal_coord p_xhyhbond_nbd p_orthonormal_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4016 Nucleic Acid Atoms Solvent Atoms 787 Heterogen Atoms 329
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling