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Rice L-galactose dehydrogenase (holo form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EZI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M bis-tris pH 6.5, 0.2M MgCl2, 25% poly- ethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.09 41.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.838 α = 90 b = 55.17 β = 101.529 c = 56.911 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 210 2012-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 1.8 50 99.6 0.104 35.3 7 27173
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 1.8 1.83 0.878 2.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7EZI 1.8 32.797 26974 1359 99.587 0.211 0.2089 0.2082 0.2573 0.2562 37.347
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] -0.171 0.367 0.212 -0.176
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.436 r_dihedral_angle_4_deg 21.684 r_dihedral_angle_3_deg 15.845 r_lrange_it 7.787 r_dihedral_angle_1_deg 6.376 r_scangle_it 5.782 r_mcangle_it 4.459 r_scbond_it 3.847 r_mcbond_it 3.116 r_angle_refined_deg 1.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.436 r_dihedral_angle_4_deg 21.684 r_dihedral_angle_3_deg 15.845 r_lrange_it 7.787 r_dihedral_angle_1_deg 6.376 r_scangle_it 5.782 r_mcangle_it 4.459 r_scbond_it 3.847 r_mcbond_it 3.116 r_angle_refined_deg 1.513 r_nbtor_refined 0.309 r_nbd_refined 0.221 r_symmetry_nbd_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.165 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.108 r_gen_planes_refined 0.009 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2425 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing