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Haloferax mediterranei glucose dehydrogenase in complex with NADP, Zn and glucose.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B5V PDB ENTRY 2B5V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 1.5M SODIUM CITRATE, 0.1M SODIUM HEPES PH8.0, 10MM NADP, pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.3 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.492 α = 90 b = 112.703 β = 90 c = 151.452 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 290 IMAGE PLATE MARRESEARCH MIRRORS 2001-01-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 2.03 30 98.9 0.08 18.3 6.8 34033
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 2.03 2.08 89.9 0.28 3.7 2.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2B5V 2.03 14.87 32242 1718 99 0.135 0.134 0.159 0.1741 RANDOM 29.38
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] 0.01 -0.04 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.103 r_dihedral_angle_4_deg 14.371 r_dihedral_angle_3_deg 11.605 r_scangle_it 10.403 r_scbond_it 7.774 r_mcbond_it 7.405 r_mcangle_it 7.19 r_dihedral_angle_1_deg 5.287 r_angle_refined_deg 1.224 r_angle_other_deg 0.872
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.103 r_dihedral_angle_4_deg 14.371 r_dihedral_angle_3_deg 11.605 r_scangle_it 10.403 r_scbond_it 7.774 r_mcbond_it 7.405 r_mcangle_it 7.19 r_dihedral_angle_1_deg 5.287 r_angle_refined_deg 1.224 r_angle_other_deg 0.872 r_symmetry_vdw_other 0.206 r_nbd_refined 0.198 r_nbd_other 0.19 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.156 r_symmetry_vdw_refined 0.15 r_nbtor_other 0.084 r_symmetry_hbond_refined 0.076 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2770 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing