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Crystal structure of the phosphonate binding protein, PhnD, from Escherichia coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.2M Magnesium chloride hexahydrate, 0.1M Bis-tris, 25%(w/v) PEG 3,350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.91 35.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.768 α = 90 b = 64.399 β = 93.52 c = 107.688 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD RAYONIX MX225HE 2009-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97929 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 28.9 99 55563 55007
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.2 28.9 55563 52190 2798 98.8 0.20586 0.20586 0.20213 0.2008 0.2764 0.2716 RANDOM 24.347
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] -0.81 0.22 1.86 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.987 r_dihedral_angle_4_deg 19.761 r_dihedral_angle_3_deg 19.555 r_dihedral_angle_1_deg 6.693 r_scangle_it 3.903 r_scbond_it 2.595 r_angle_refined_deg 1.624 r_mcangle_it 1.456 r_mcbond_it 0.816 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.987 r_dihedral_angle_4_deg 19.761 r_dihedral_angle_3_deg 19.555 r_dihedral_angle_1_deg 6.693 r_scangle_it 3.903 r_scbond_it 2.595 r_angle_refined_deg 1.624 r_mcangle_it 1.456 r_mcbond_it 0.816 r_chiral_restr 0.11 r_bond_refined_d 0.017 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9212 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 20
Software Software Software Name Purpose SPEC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling