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Haloferax mediterranei glucose dehydrogenase in complex with NADP, Zn and gluconolactone.
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 1.4M SODIUM CITRATE, HEPES PH7.5.
Crystal Properties Matthews coefficient Solvent content 3.3 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.647 α = 90 b = 112.205 β = 90 c = 150.597 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 2001-01-18 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 30 98.9 0.05 17.4 7.7 35315
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 2.05 99.2 0.36 2.6 2.6
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 15 33477 1776 99 0.136 0.135 0.1493 0.159 0.1756 RANDOM 34.12
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.78 r_dihedral_angle_4_deg 14.379 r_dihedral_angle_3_deg 11.606 r_scangle_it 11.303 r_scbond_it 7.787 r_mcangle_it 7.428 r_mcbond_it 6.759 r_dihedral_angle_1_deg 5.322 r_angle_refined_deg 1.222 r_angle_other_deg 0.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.78 r_dihedral_angle_4_deg 14.379 r_dihedral_angle_3_deg 11.606 r_scangle_it 11.303 r_scbond_it 7.787 r_mcangle_it 7.428 r_mcbond_it 6.759 r_dihedral_angle_1_deg 5.322 r_angle_refined_deg 1.222 r_angle_other_deg 0.848 r_symmetry_vdw_other 0.219 r_nbd_refined 0.2 r_nbd_other 0.192 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.141 r_nbtor_other 0.085 r_symmetry_vdw_refined 0.082 r_chiral_restr 0.068 r_symmetry_hbond_refined 0.039 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 143 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing