☰ Navigation Tabs
Crystal structure of metallo-carboxypeptidase from Burkholderia cenocepacia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K2K PDB ENTRY 3K2K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 100 NL OF PROTEIN SOLUTION (10 MG ML-1 IN 100 MM SODIUM ACETATE PH 5.0, 150 MM NACL AND 0.5 MM ZINC SULPHATE) WERE MIXED AT 1:1 RATIO WITH RESERVOIR (0.2M LITHIUM SULPHATE, 25% PEG 3350 AND 0.1M BIS-TRIS, PH 5.5) EQUILIBRATED AGAINST A 70 UL RESERVOIR. CRYSTALS WERE OBSERVED AFTER THREE DAYS.
Crystal Properties Matthews coefficient Solvent content 2.16 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.897 α = 90 b = 85.947 β = 90 c = 289.016 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 287 CCD MARRESEARCH MIRRORS 2011-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 1.9 40 99.9 0.13 8.4 4.2 124234 2
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 1.9 2 100 0.48 2.7 4.2
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 3K2K 1.9 40 117888 6246 99.75 0.16641 0.16439 0.165 0.20455 0.205 RANDOM 16.436
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] -0.57 1.11 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.897 r_dihedral_angle_4_deg 16.01 r_dihedral_angle_3_deg 13.856 r_dihedral_angle_1_deg 5.801 r_angle_refined_deg 1.143 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.897 r_dihedral_angle_4_deg 16.01 r_dihedral_angle_3_deg 13.856 r_dihedral_angle_1_deg 5.801 r_angle_refined_deg 1.143 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 11931 Nucleic Acid Atoms Solvent Atoms 1049 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing