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Crystal structure of a putative dehydrogenase from Burkholderia cenocepacia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IQG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 289 BuceA.00010.a.B1 PS01733 at 22.8 mg/mL against JCSG+ screen condition D11, 140 mM CaCl2, 70 mM NaOAc pH 4.6, 14% isopropanol, 30% glycerol, crystal tracking ID 242030d11, unique puck ID smk5-3, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.18 43.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.89 α = 90 b = 102.81 β = 90 c = 123.09 γ = 90
Symmetry Space Group F 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 ADSC QUANTUM 315r 2013-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.12709 SSRL BL7-1
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 1.85 20 99.7 0.06 19.58 4.5 20185 20122 -3 27.516
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 1.85 1.9 99.5 0.495 3.32
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 4IQG 1.85 19.75 20060 1021 99.38 0.1526 0.1503 0.1647 0.1986 0.2105 RANDOM 25.6368
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] 3.74 -1.59 -2.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.09 r_dihedral_angle_4_deg 16.557 r_dihedral_angle_3_deg 12.181 r_dihedral_angle_1_deg 5.617 r_mcangle_it 2.022 r_angle_refined_deg 1.528 r_mcbond_it 1.379 r_mcbond_other 1.349 r_angle_other_deg 0.835 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.09 r_dihedral_angle_4_deg 16.557 r_dihedral_angle_3_deg 12.181 r_dihedral_angle_1_deg 5.617 r_mcangle_it 2.022 r_angle_refined_deg 1.528 r_mcbond_it 1.379 r_mcbond_other 1.349 r_angle_other_deg 0.835 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1672 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 14
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection XDS data reduction