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Crystal structure of YgiN from Escherichia coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 295 Ammonium Sulphate, Tri-Sodium Citrate, Sodium/Potassium Tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.43 64.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.057 α = 90 b = 102.057 β = 90 c = 102.057 γ = 90
Symmetry Space Group P 41 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 ADSC QUANTUM 4 2002-04-25 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARRESEARCH 2003-04-11 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 1.199998 CHESS F1 2 SYNCHROTRON NSLS BEAMLINE X9A 0.979383, 0.979228, 0.971708 NSLS X9A
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 2.2 50 99.7 9700 9700 2 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 2.2 2.28 99.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MAD THROUGHOUT 2.2 19.65 2 9700 9700 467 100 0.21031 0.21031 0.20842 0.2008 0.24948 0.2343 RANDOM 37.566
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 r_scangle_it 7.551 r_dihedral_angle_1_deg 6.951 r_scbond_it 4.66 r_mcangle_it 3.012 r_angle_refined_deg 2.33 r_mcbond_it 1.666 r_angle_other_deg 1.037 r_symmetry_vdw_other 0.445 r_symmetry_vdw_refined 0.284 r_nbd_refined 0.269
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 7.551 r_dihedral_angle_1_deg 6.951 r_scbond_it 4.66 r_mcangle_it 3.012 r_angle_refined_deg 2.33 r_mcbond_it 1.666 r_angle_other_deg 1.037 r_symmetry_vdw_other 0.445 r_symmetry_vdw_refined 0.284 r_nbd_refined 0.269 r_nbd_other 0.256 r_xyhbond_nbd_refined 0.213 r_chiral_restr 0.153 r_nbtor_other 0.102 r_symmetry_hbond_refined 0.062 r_bond_refined_d 0.04 r_gen_planes_refined 0.012 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 797 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SHELXD phasing