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Crystal structure of NAD-binding phosphogluconate dehydrogenase-like protein from Alicyclobacillus acidocaldarius
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other different crystal form of the same protein (solved by SAD)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 297 12% PEG6K, 2 M NaCl, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.4 48.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.838 α = 90 b = 61.005 β = 112.16 c = 50.068 γ = 90
Symmetry Space Group C 1 2 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 mirrors 2010-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97926 APS 19-ID
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 1.9 50 99.6 0.065 25.1 3.7 25141 25034 -3 35.41
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) 1.9 1.93 99.4 0.421 2.5 3.5
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 different crystal form of the same protein (solved by SAD) 1.9 21.99 25015 25015 1271 0.1859 0.185 0.185 0.201 0.1967 RANDOM 49.09
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] 3.6729 -1.5544 4.485 -8.1579
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.47 t_omega_torsion 3.3 t_angle_deg 1.09 t_bond_d 0.012 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.47 t_omega_torsion 3.3 t_angle_deg 1.09 t_bond_d 0.012 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2095 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 2
Software Software Software Name Purpose SBC-Collect data collection PHASER phasing PHENIX refinement BUSTER refinement HKL-3000 data reduction HKL-3000 data scaling