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Crystal structure of Cryptosporidium parvum adenylate kinase cgd5_3360
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AK2 PDB entry 1AK2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 2.5 M Ammonium sulfate, 0.1 M BTP pH 7.0, 10 mM Adenosine-5-pentaphosphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.99 58.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.175 α = 90 b = 101.175 β = 90 c = 72.433 γ = 120
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 315 2007-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97934 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 20 99 0.067 0.057 11 3.6 36167 36167 19.543
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 100 0.466 0.438 3.35 3.7 3686
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1AK2 1.6 19.37 36130 36130 1814 98.98 0.164 0.162 0.1613 0.202 0.2006 RANDOM 25.453
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] 0.02 0.01 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.836 r_dihedral_angle_4_deg 18.141 r_dihedral_angle_3_deg 15.529 r_dihedral_angle_1_deg 6.95 r_scangle_it 5.429 r_scbond_it 3.965 r_angle_refined_deg 2.939 r_mcangle_it 2.748 r_mcbond_it 1.98 r_symmetry_hbond_refined 0.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.836 r_dihedral_angle_4_deg 18.141 r_dihedral_angle_3_deg 15.529 r_dihedral_angle_1_deg 6.95 r_scangle_it 5.429 r_scbond_it 3.965 r_angle_refined_deg 2.939 r_mcangle_it 2.748 r_mcbond_it 1.98 r_symmetry_hbond_refined 0.412 r_chiral_restr 0.37 r_nbtor_refined 0.319 r_symmetry_vdw_refined 0.268 r_nbd_refined 0.225 r_xyhbond_nbd_refined 0.213 r_bond_refined_d 0.035 r_gen_planes_refined 0.017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1655 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 70
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection