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Crystal structure of a putative deoxyribose-phosphate aldolase from Coccidioides immitis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NGJ 3NGJ molecule A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 4.93 mg/mL CoimA.00559.a.A1 PS00460 against Hampton Index Screen condition G9, 0.2 M ammonium sulphate, 0.1 M Tris pH 8.5, 25% PEG 3350 enheanced with 20% glycerol as cryo-protectant, crystal tracking ID 216774g9, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.16 42.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.69 α = 90 b = 80.81 β = 102.99 c = 71.67 γ = 90
Symmetry Space Group P 1 21 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 2010-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.97946 ALS 5.0.3
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 1.6 50 98 0.051 19.41 5 69876 68464 -3 23.315
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) 1.6 1.64 96.5 0.385 4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3NGJ molecule A 1.6 50 68409 3443 97.95 0.1646 0.163 0.1944 0.193 RANDOM 21.0965
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] -0.51 -0.22 0.06 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.615 r_dihedral_angle_4_deg 16.73 r_dihedral_angle_3_deg 10.96 r_dihedral_angle_1_deg 5.855 r_scangle_it 2.925 r_scbond_it 1.7 r_angle_refined_deg 1.237 r_mcangle_it 1.014 r_mcbond_it 0.546 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.615 r_dihedral_angle_4_deg 16.73 r_dihedral_angle_3_deg 10.96 r_dihedral_angle_1_deg 5.855 r_scangle_it 2.925 r_scbond_it 1.7 r_angle_refined_deg 1.237 r_mcangle_it 1.014 r_mcbond_it 0.546 r_chiral_restr 0.082 r_bond_refined_d 0.016 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3752 Nucleic Acid Atoms Solvent Atoms 507 Heterogen Atoms 8
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction