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Crystal Structure of the computationally designed serine hydrolase 3mmj_2, Northeast Structural Genomics Consortium (NESG) Target OR318
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U26 PDB ENTRY 1U26
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10 273 Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: Ammonium phosphate-monobasic 0.1M, CAPS 0.1M, PEG 2000 12% (w/v), VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.46 49.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.243 α = 90 b = 194.552 β = 90 c = 46.09 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 MAR CCD 165 mm 2013-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.97908 NSLS X4C
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 30 85.4 0.09 16.9 6.3 43119 -3 15.83
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 1U26 2.005 29.732 1.43 42747 1988 84.51 0.204 0.202 0.2024 0.261 0.2593 26.531
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 16.177 f_angle_d 1.174 f_chiral_restr 0.087 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5077 Nucleic Acid Atoms Solvent Atoms 510 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction SCALEPACK data scaling BALBES phasing