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Crystal structure of a putative phosphonomutase from Burkholderia cenocepacia J2315
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZE3 PDB entry 2ZE3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 289 JCSG+c2: 20% PEG6000, 1M LiCl, 0.1M NaCit pH4.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.47 50.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 218.6 α = 90 b = 91.18 β = 91.53 c = 110.01 γ = 90
Symmetry Space Group C 1 2 1
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 RAYONIX MX-300 2013-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9798 APS 21-ID-F
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 1.7 50 99.8 0.055 17.15 3.76 236885 236354 14.8
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 1.7 1.74 99.9 0.439 3.51 3.78 17451
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 2ZE3 1.7 46.29 224512 11843 99.77 0.15911 0.15752 0.169 0.18912 0.1964 RANDOM 21.112
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] -0.61 0.66 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.964 r_dihedral_angle_4_deg 18.159 r_dihedral_angle_3_deg 11.925 r_long_range_B_refined 6.042 r_long_range_B_other 6.042 r_dihedral_angle_1_deg 5.466 r_scangle_other 3.319 r_scbond_it 2.115 r_scbond_other 2.114 r_mcangle_it 2.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.964 r_dihedral_angle_4_deg 18.159 r_dihedral_angle_3_deg 11.925 r_long_range_B_refined 6.042 r_long_range_B_other 6.042 r_dihedral_angle_1_deg 5.466 r_scangle_other 3.319 r_scbond_it 2.115 r_scbond_other 2.114 r_mcangle_it 2.064 r_mcangle_other 2.064 r_angle_refined_deg 1.621 r_mcbond_it 1.317 r_mcbond_other 1.317 r_angle_other_deg 0.855 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14455 Nucleic Acid Atoms Solvent Atoms 1797 Heterogen Atoms 41
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling