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Rice L-galactose dehydrogenase (apo form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LUT
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 2.02 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.745 α = 90 b = 54.877 β = 102.268 c = 56.753 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 270 2012-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.0000 Photon Factory BL-1A
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 1.2 100 99.1 0.077 17.4 7 87015
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 1.2 1.22 0.611 4.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3LUT 1.2 32.092 86970 4348 99.245 0.153 0.1516 0.1872 0.2047 18.964
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] 1.537 -0.028 -0.563 -0.879
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.509 r_dihedral_angle_4_deg 21 r_dihedral_angle_3_deg 12.055 r_rigid_bond_restr 7.38 r_dihedral_angle_1_deg 5.97 r_scangle_it 3.874 r_scbond_it 3.706 r_lrange_it 3.334 r_mcangle_it 2.373 r_angle_refined_deg 2.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.509 r_dihedral_angle_4_deg 21 r_dihedral_angle_3_deg 12.055 r_rigid_bond_restr 7.38 r_dihedral_angle_1_deg 5.97 r_scangle_it 3.874 r_scbond_it 3.706 r_lrange_it 3.334 r_mcangle_it 2.373 r_angle_refined_deg 2.145 r_mcbond_it 2.051 r_nbtor_refined 0.314 r_symmetry_xyhbond_nbd_refined 0.236 r_nbd_refined 0.213 r_symmetry_nbd_refined 0.192 r_xyhbond_nbd_refined 0.178 r_chiral_restr 0.134 r_metal_ion_refined 0.024 r_bond_refined_d 0.017 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2470 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing