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Haloferax mediterranei glucose dehydrogenase in complex with NADPH and Zn.
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 70% 2-METHYL-2,4,-PENTANEDIOL, 1MM NADPH, 1MM ZNCL2, 100MM HEPES PH7.5
Crystal Properties Matthews coefficient Solvent content 3.2 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.569 α = 90 b = 107.725 β = 90 c = 153.646 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 100 IMAGE PLATE MARRESEARCH YALE MIRRORS 2001-07-26 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 2.01 30 94.5 0.06 30.1 3.9 32173
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 2.01 2.08 82.5 0.35 3.7 3.4
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 PDB ENTRY 2B5V 2.01 19.84 30211 1631 94.5 0.186 0.184 0.1828 0.222 0.2159 RANDOM 31.07
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] 0.06 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.876 r_dihedral_angle_4_deg 14.354 r_dihedral_angle_3_deg 11.766 r_mcbond_it 5.878 r_dihedral_angle_1_deg 5.67 r_mcangle_it 5.615 r_scbond_it 5.399 r_scangle_it 4.687 r_angle_refined_deg 1.287 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.876 r_dihedral_angle_4_deg 14.354 r_dihedral_angle_3_deg 11.766 r_mcbond_it 5.878 r_dihedral_angle_1_deg 5.67 r_mcangle_it 5.615 r_scbond_it 5.399 r_scangle_it 4.687 r_angle_refined_deg 1.287 r_nbtor_refined 0.301 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.184 r_xyhbond_nbd_refined 0.15 r_symmetry_hbond_refined 0.138 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 245 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing