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Structural Genomics of Caenorhabditis elegans : Dihydropteridine reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DHR PDB entry 1DHR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 295 pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
RESERVOIR: 20% PEG8000, 10 MM MGCL2, 0.1 M AMMONIUM SULFATE, 50 MM MES, PH 5.6;
PROTEIN STOCK: 17.3 MG/ML IN 10 MM HEPES, PH 7.0; DROPS: 2 MICROLITERS OF PROTEIN STOCK + 4 MICROLITERS
OF RESERVOIR SOLUTION
Crystal Properties Matthews coefficient Solvent content 2.05 39.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.926 α = 89.98 b = 50.892 β = 71.98 c = 58.77 γ = 82.05
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 MAR CCD 165 mm 2002-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.07175 APS 22-ID
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 1.6 50 93.9 0.041 10 1.9 56662 56662 -3 18.1
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) 1.6 1.64 74 0.281 3.1 0.8 2969
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 (All) 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 1DHR 1.65 32.28 52498 52498 2680 95.3 0.201 0.201 0.194 0.1959 0.227 0.2267 RANDOM 16.1
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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.3 c_scangle_it 2.5 c_scbond_it 1.81 c_mcangle_it 1.57 c_angle_deg 1.2 c_mcbond_it 1.09 c_improper_angle_d 0.88 c_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3488 Nucleic Acid Atoms Solvent Atoms 601 Heterogen Atoms 24
Software Software Software Name Purpose CNS refinement MAR345 data collection HKL-2000 data scaling AMoRE phasing