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Structure of a dye-linked L-proline dehydrogenase mutant from the aerobic hyperthermophilic archaeon, Aeropyrum pernix
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AXB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 sitting drop 6.5 293 PEG8000, Mg acetate, Mes, pH 6.5, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.19 43.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.987 α = 71.65 b = 70.57 β = 70.85 c = 73.092 γ = 70.15
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 Rhodium coated silicon single crystal 2012-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.01 50 99.9 52556 52556
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.04 93.2
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 3AXB 2.01 24.2 52556 52556 2654 0.2126 0.2126 0.2103 0.2121 0.2551 0.2525 RANDOM 38.6857
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] 2.33 0.52 -0.18 -2.41 1.22 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.979 r_dihedral_angle_4_deg 23.587 r_dihedral_angle_3_deg 20.156 r_dihedral_angle_1_deg 6.919 r_angle_refined_deg 2.023 r_chiral_restr 0.148 r_bond_refined_d 0.019 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6550 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 130
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling