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Crystal Structure and Activity Studies of Escherichia Coli Yadb ORF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GLN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 PEG4000, MPD, Nacacodylate, pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 41.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.92 α = 90 b = 39.3 β = 116.19 c = 69.15 γ = 90
Symmetry Space Group C 1 2 1
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 2002-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.5 62.02 99.4 0.057 9.1 3.7 43648
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) 1.5 1.58 99.4 0.283 2.5 3.5
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1GLN 1.5 24.254 40227 40227 3063 96 0.1472 0.14729 0.14559 0.1665 0.16969 RANDOM 12.591
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] -0.99 -1.04 -0.07 0.14
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 7.6 r_dihedral_angle_1_deg 5.145 r_scangle_it 3.699 r_scbond_it 2.426 r_sphericity_bonded 2.376 r_mcangle_it 1.601 r_angle_refined_deg 1.204 r_mcbond_it 0.967 r_angle_other_deg 0.835 r_rigid_bond_restr 0.618
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 7.6 r_dihedral_angle_1_deg 5.145 r_scangle_it 3.699 r_scbond_it 2.426 r_sphericity_bonded 2.376 r_mcangle_it 1.601 r_angle_refined_deg 1.204 r_mcbond_it 0.967 r_angle_other_deg 0.835 r_rigid_bond_restr 0.618 r_symmetry_vdw_other 0.288 r_symmetry_vdw_refined 0.284 r_nbd_other 0.237 r_symmetry_hbond_refined 0.228 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.08 r_nbtor_other 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2163 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling