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Crystal structure of the native E. coli zinc amidase AmiD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BH7 PDB ENTRY 2BH7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 1M LICL, 10 % PEG 6K, 0.1M ZNCL2, PH 4
Crystal Properties Matthews coefficient Solvent content 3.19 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.99 α = 90 b = 88.99 β = 90 c = 183.923 γ = 120
Symmetry Space Group P 61 2 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 MARRESEARCH 2004-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 1.8 21.38 98 0.08 22.5 8.9 41725 2 19.7
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 1.8 1.9 99.6 0.41 3.7 6.8
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 PDB ENTRY 2BH7 1.8 21.23 36115 4027 98.26 0.16302 0.16077 0.1592 0.18367 0.1825 RANDOM 15.313
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] 0.54 0.27 0.54 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.761 r_dihedral_angle_3_deg 12.471 r_dihedral_angle_4_deg 11.795 r_dihedral_angle_1_deg 5.659 r_scangle_it 3.383 r_mcangle_it 2.38 r_scbond_it 2.186 r_mcbond_it 1.797 r_angle_refined_deg 1.403 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.761 r_dihedral_angle_3_deg 12.471 r_dihedral_angle_4_deg 11.795 r_dihedral_angle_1_deg 5.659 r_scangle_it 3.383 r_mcangle_it 2.38 r_scbond_it 2.186 r_mcbond_it 1.797 r_angle_refined_deg 1.403 r_nbtor_refined 0.298 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.127 r_metal_ion_refined 0.113 r_symmetry_hbond_refined 0.103 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2056 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing