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Crystal structure of Escherichia coli gene product Yecd at 1.3 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NBA PDB entries 1NBA and 1IM5 experimental model PDB 1IM5 PDB entries 1NBA and 1IM5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 5.5 293 MPD, TRIS, acetate, NaCl, Lysine, pH 5.5, EVAPORATION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.03 39.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.502 α = 90 b = 108.886 β = 90 c = 50.419 γ = 90
Symmetry Space Group P 21 21 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 2002-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 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 1.3 50.77 85.9 0.059 6.4 5.5 190258 163406 3 18.62
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 1.3 1.35 72.6 0.064 2.5 13256
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 (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 PDB entries 1NBA and 1IM5 1.3 50.77 162173 155206 8200 85.89 0.14596 0.14499 0.1467 0.16494 0.1665 RANDOM 11.354
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] -0.5 -0.03 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.611 r_scangle_it 3.092 r_scbond_it 1.926 r_angle_refined_deg 1.399 r_mcangle_it 1.263 r_angle_other_deg 0.83 r_mcbond_it 0.691 r_symmetry_vdw_other 0.271 r_nbd_other 0.253 r_nbd_refined 0.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.611 r_scangle_it 3.092 r_scbond_it 1.926 r_angle_refined_deg 1.399 r_mcangle_it 1.263 r_angle_other_deg 0.83 r_mcbond_it 0.691 r_symmetry_vdw_other 0.271 r_nbd_other 0.253 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.19 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.083 r_nbtor_other 0.083 r_gen_planes_other 0.012 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 5751 Nucleic Acid Atoms Solvent Atoms 924 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling TRUNCATE data scaling T-COFFEE phasing MODELLER phasing AMoRE phasing