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Crystal structures of a putative dihydrodipicolinate synthase family protein from Coccidioides immitis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 CoimA.00447.a.A1 PW28367 at 24.64 mg/mL against CSHT screen condition B2, 0.2 M CaCl2, 0.1 M Na Hepes pH 7.5, 28% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.22 61.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.76 α = 90 b = 89.76 β = 90 c = 371.46 γ = 120
Symmetry Space Group P 65 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 2010-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 2.35 50 99.6 0.085 27.2 19.7 38337 38200 -3 46.203
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) 2.35 2.41 100 0.513 5.67 17.8 2749
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 2v8z 2.35 50 38011 1902 99.17 0.201 0.1993 0.198 0.2336 0.2344 RANDOM 40.6171
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] 2.34 1.17 2.34 -3.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.195 r_dihedral_angle_4_deg 15.685 r_dihedral_angle_3_deg 14.7 r_dihedral_angle_1_deg 5.972 r_scangle_it 3.372 r_scbond_it 2.041 r_mcangle_it 1.4 r_angle_refined_deg 1.32 r_mcbond_it 0.748 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.195 r_dihedral_angle_4_deg 15.685 r_dihedral_angle_3_deg 14.7 r_dihedral_angle_1_deg 5.972 r_scangle_it 3.372 r_scbond_it 2.041 r_mcangle_it 1.4 r_angle_refined_deg 1.32 r_mcbond_it 0.748 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4393 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 16
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction