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The structure of the Escherichia coli murein tripeptide binding protein MppA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z23 PDB ENTRY 2Z23
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 293 20% PEG3350, 50mM zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.59 52.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.074 α = 90 b = 165.074 β = 90 c = 38.167 γ = 120
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 315r TOROIDAL FOCUSING MIRROR 2009-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.06 50 92 0.107 20.6 9.7 34597
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 2.06 2.1 33.5 0.553 1.6 4.3
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 ENTRY 2Z23 2.07 41.27 32851 32850 1743 100 0.17429 0.17195 0.1754 0.21813 0.2199 RANDOM 24.863
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] -0.02 -0.01 -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.593 r_dihedral_angle_4_deg 15.974 r_dihedral_angle_3_deg 15.318 r_scangle_it 7.858 r_dihedral_angle_1_deg 6.175 r_scbond_it 6.107 r_mcangle_it 4.38 r_mcbond_it 3.092 r_angle_refined_deg 1.896 r_mcbond_other 1.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.593 r_dihedral_angle_4_deg 15.974 r_dihedral_angle_3_deg 15.318 r_scangle_it 7.858 r_dihedral_angle_1_deg 6.175 r_scbond_it 6.107 r_mcangle_it 4.38 r_mcbond_it 3.092 r_angle_refined_deg 1.896 r_mcbond_other 1.123 r_angle_other_deg 1.022 r_chiral_restr 0.12 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4038 Nucleic Acid Atoms Solvent Atoms 338 Heterogen Atoms 31
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling