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CRYSTAL STRUCTURE OF E. COLI PROTEIN YDDE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other YDDE SOLVED BY SAD ON SE-MET EDGE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 20% PEG 600, 0.1 M IMIDAZOLE-MALATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.7 53.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.159 α = 90 b = 79.631 β = 115.26 c = 77.022 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 100 CCD ADSC QUANTUM 4 2002-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9330,0.9340 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 2 20 94.6 0.044 12 2.7 49349
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 2 2.05 94.6 0.431 1.7 2.6
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 (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 YDDE SOLVED BY SAD ON SE-MET EDGE 2 20 44289 2407 94.07 0.18838 0.18626 0.2084 0.22761 0.2407 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] 0.28 -1.69 1.21 -2.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.117 r_scangle_it 2.453 r_scbond_it 1.457 r_angle_refined_deg 1.201 r_mcangle_it 0.953 r_angle_other_deg 0.767 r_mcbond_it 0.52 r_symmetry_vdw_other 0.271 r_nbd_other 0.237 r_nbd_refined 0.191
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.117 r_scangle_it 2.453 r_scbond_it 1.457 r_angle_refined_deg 1.201 r_mcangle_it 0.953 r_angle_other_deg 0.767 r_mcbond_it 0.52 r_symmetry_vdw_other 0.271 r_nbd_other 0.237 r_nbd_refined 0.191 r_xyhbond_nbd_refined 0.165 r_symmetry_vdw_refined 0.082 r_nbtor_other 0.08 r_chiral_restr 0.073 r_symmetry_hbond_refined 0.058 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_xyhbond_nbd_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4610 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALA data scaling MOLREP phasing REFMAC refinement CCP4 data scaling