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Apo form of the soluble PQQ-dependent Glucose Dehydrogenase from Acinetobacter calcoaceticus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C9U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 PEG 4000 (12%)
100 mM TRIS pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.36 47.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.407 α = 88.04 b = 54.898 β = 81.58 c = 85.474 γ = 69.62
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 200K OSMIC VARIMAX HF 2014-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.54187
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 1.76 25.73 91.6 9.42 3.07 83379
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 1C9U 1.76 25.73 83379 4137 91.74 0.1795 0.1776 0.1692 0.2144 0.2043 RANDOM 20.23
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] 0.6439 -1.2862 0.4221 -1.8344 0.217 1.1905
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.14 t_omega_torsion 4.02 t_angle_deg 1.06 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.14 t_omega_torsion 4.02 t_angle_deg 1.06 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle 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 7073 Nucleic Acid Atoms Solvent Atoms 1099 Heterogen Atoms 7
Software Software Software Name Purpose XSCALE data scaling PHASER phasing BUSTER-TNT refinement PDB_EXTRACT data extraction XSCALE data reduction PHASER phasing BUSTER refinement