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Crystal structure of BaLdcB / VanY-like L,D-carboxypeptidase Zinc(II)-free
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F78 PDB ENTRY 4F78
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 Protein: 2.3mg/mL, 0.3M Sodium cloride, 0.1M 0.1M HEPES pH 7.5;
Screen: 0.1M HEPES pH 7.0, 30% Jeffamine ED-2001;
Cryo: paraton., VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.66 53.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.576 α = 90 b = 112.996 β = 90 c = 124.659 γ = 90
Symmetry Space Group I 2 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 MARMOSAIC 300 mm CCD Beryllium lenses 2013-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.3 30 98.3 0.093 13.5 4.2 24059 24059 -3
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 2.3 2.34 94.3 0.542 2.4 3.6
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 4F78 2.3 29.71 22730 22730 1226 98.16 0.19442 0.19099 0.1927 0.25873 0.2594 RANDOM 37.013
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] -4.27 7.02 -2.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.009 r_dihedral_angle_4_deg 12.902 r_dihedral_angle_3_deg 10.488 r_scangle_it 5.23 r_scbond_it 3.619 r_dihedral_angle_1_deg 2.655 r_mcangle_it 2.065 r_angle_refined_deg 1.364 r_mcbond_it 1.221 r_angle_other_deg 0.797
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.009 r_dihedral_angle_4_deg 12.902 r_dihedral_angle_3_deg 10.488 r_scangle_it 5.23 r_scbond_it 3.619 r_dihedral_angle_1_deg 2.655 r_mcangle_it 2.065 r_angle_refined_deg 1.364 r_mcbond_it 1.221 r_angle_other_deg 0.797 r_mcbond_other 0.359 r_chiral_restr 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 2912 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 4
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling