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Crystal Structure of Mandelate racemase/muconate lactonizing enzyme from a Marine actinobacterium in complex with magnesium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MSY PDB ID: 3MSY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 0.2M Magnesium Chloride
0.1M Hepes pH 7.5, 20% PEG 3350, 0.025M ethylenediamine-tetraacetic disodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.13 42.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.961 α = 115.8 b = 90.103 β = 109.75 c = 94.66 γ = 97.58
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 mirrors 2010-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9792 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.16 50 98.1 0.084 19.1 0.9 117788 117788 11.1
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 2.16 2.24 96.6 0.19 10.8 3.9 11562
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 (All) 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 ID: 3MSY 2.16 42.51 115558 115558 4670 96 0.212 0.207 0.207 0.2021 0.24 0.2337 RANDOM 21.7
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] 4.55 0.19 3.19 -2.89 -0.43 -1.66
RMS Deviations Key Refinement Restraint Deviation c_dihedral_degree 22.3 c_angle_deg 1.4 c_improper_angle_deg 0.82 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16538 Nucleic Acid Atoms Solvent Atoms 626 Heterogen Atoms 6
Software Software Software Name Purpose CBASS data collection MOLREP phasing CNS refinement DENZO data reduction HKL-2000 data scaling