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Crystal structure of PhzD protein active site mutant with substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Native structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 10-20% polyethylene glycol 4000, 0.2M ammonium formate, 0.2% beta-octylglucoside, 1mM isochorismate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.02 47.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.4 α = 90 b = 77.01 β = 90 c = 82.44 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 IMAGE PLATE RIGAKU RAXIS IV++ OSMIC 2002-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 1.6 20 99.7 0.042 22 3 27572
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.7 99 0.207 3.1 3 3895
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 FREE R Native structure 1.6 20 27403 27403 1423 92.9 0.134 0.134 0.134 0.1401 0.21 0.2116 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 1608 1962
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.08 s_similar_adp_cmpnt 0.055 s_non_zero_chiral_vol 0.049 s_zero_chiral_vol 0.047 s_from_restr_planes 0.0279 s_angle_d 0.026 s_anti_bump_dis_restr 0.021 s_bond_d 0.008 s_rigid_bond_adp_cmpnt 0.003 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1629 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 36
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement CrystalClear data reduction d*TREK data scaling SHELX phasing