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N-acetylmuramoyl-L-alanine amidase AmiC2 of Nostoc punctiforme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JWQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 1 microL of protein (3.7 mg/ml) was mixed with 1 microL of well solution containing 120 mM alcohols (mixture of 1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, and 1,3-propanediol), 100 mM MES/imidazole at pH 6.5, and 37.5 % PEG1000/PEG3350/MPD
Crystal Properties Matthews coefficient Solvent content 1.81 32.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.03 α = 90 b = 62.76 β = 90 c = 65.29 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS3 2M 2014-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.12 50 94.3 1 31.54 11.8 52924 13.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.12 1.15 69.3 0.884 3.65 6.58
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1jwq 1.12 45.246 1.36 52922 2647 94.32 0.1348 0.1342 0.1345 0.146 0.1456
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 f_dihedral_angle_d 13.3 f_angle_d 1.492 f_chiral_restr 0.079 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1387 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing