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Crystal structure of a response regulator protein from Burkholderia pseudomallei with a phosphorylated aspartic acid, calcium ion and citrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZY2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 289 BupsA.00608.a.A1 PW30798 at 30.69 mg/mL against JCSG+ screen condition A6, 0.2 M Li2SO4, 0.1 M phosphate/citrate pH 4.2, 20% PEG 1000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 220922a6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.08 40.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.24 α = 90 b = 55.24 β = 90 c = 95.42 γ = 120
Symmetry Space Group P 31 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 ADSC QUANTUM 315r 2011-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97740 ALS 5.0.1
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 1.7 50 99.5 0.049 23.22 6.2 19149 19044 -3 25.389
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) 1.7 1.74 99.8 0.509 3.76 5.1 1393
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 1zy2 1.7 50 19018 976 99.12 0.2081 0.2064 0.2213 0.2395 0.257 RANDOM 24.9592
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] -0.81 -0.41 -0.81 1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.372 r_dihedral_angle_4_deg 13.979 r_dihedral_angle_3_deg 12.393 r_dihedral_angle_1_deg 5.133 r_scangle_it 3.921 r_scbond_it 2.415 r_angle_refined_deg 1.486 r_mcangle_it 1.399 r_mcbond_it 0.794 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.372 r_dihedral_angle_4_deg 13.979 r_dihedral_angle_3_deg 12.393 r_dihedral_angle_1_deg 5.133 r_scangle_it 3.921 r_scbond_it 2.415 r_angle_refined_deg 1.486 r_mcangle_it 1.399 r_mcbond_it 0.794 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1261 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 30
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction