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Crystal Structure of Apo-glyceraldehyde 3-phosphate dehydrogenase from Cryptosporidium parvum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K3T PDB ENTRY 1K3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 298 20% PEG 3000, pH 7.5, vapor diffusion, hanging drop, temperature 298K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.28 46.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.359 α = 90 b = 121.646 β = 92.31 c = 80.003 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 103 CCD MAR300 2004-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 50 98.8 0.067 9.6 2.7 68051 23.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 97.5 0.182 2.2
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 PDB ENTRY 1K3T 2.2 39.97 66477 3382 98.9 0.203 0.203 0.203 0.245 0.2445 RANDOM 34.3
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] 2.06 -1.24 2.87 -4.94
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.3 c_scangle_it 4.49 c_scbond_it 3.37 c_mcangle_it 2.71 c_mcbond_it 1.9 c_angle_deg 1.3 c_improper_angle_d 0.71 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.3 c_scangle_it 4.49 c_scbond_it 3.37 c_mcangle_it 2.71 c_mcbond_it 1.9 c_angle_deg 1.3 c_improper_angle_d 0.71 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9724 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling CNS phasing