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Crystal Structure Analysis of yibF from E. Coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 298 5 microL protein in 50 mM HEPES pH 7.5, 1 mM DTT, 4 microL reservoir (0.1M Na acetate pH 4.6,1M ammonium phosphate monobasic), 1 microL 100mM glutathione pH 7.0, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.55 51.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.34 α = 90 b = 111.34 β = 90 c = 111.34 γ = 90
Symmetry Space Group P 43 3 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 MARMOSAIC 225 mm CCD 2007-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D APS 21-ID-D
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 1.05 50 98.1 0.069 16.2 7.8 107437
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 1.05 1.09 99.7 0.465 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R NONE 1.05 26 107373 5366 93.3 0.1317 0.1528 0.163 RANDOM 16.7281
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 24 1584 1876.55
RMS Deviations Key Refinement Restraint Deviation s_anti_bump_dis_restr 0.213 s_non_zero_chiral_vol 0.099 s_approx_iso_adps 0.099 s_zero_chiral_vol 0.08 s_similar_adp_cmpnt 0.053 s_angle_d 0.033 s_from_restr_planes 0.0268 s_bond_d 0.016 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1587 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 33
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing SHELX refinement PDB_EXTRACT data extraction HKL-2000 data reduction ARP/wARP model building SHELXL-97 refinement