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Crystal structure of a mycobacterium aldo-keto reductase in its apo and liganded form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VBJ PDB ENTRY 1VBJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.1 20% PEG 0.2M CACL2 0.1M NA CACODYLATE PH 5.1
Crystal Properties Matthews coefficient Solvent content 2.2 44.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.543 α = 90 b = 103.677 β = 90 c = 112.051 γ = 90
Symmetry Space Group P 21 21 21
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 RIGAKE 2006-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 1.9 26.3 100 0.07 9.3 4.4 40896 2
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 1.9 2 100 0.33 2.3 4.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1VBJ 1.9 50 38786 2047 99.95 0.17005 0.16796 0.1674 0.20941 0.2077 RANDOM 14.078
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] -1.01 -1.16 2.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.134 r_dihedral_angle_4_deg 13.665 r_dihedral_angle_3_deg 13.607 r_dihedral_angle_1_deg 5.68 r_scangle_it 4.635 r_scbond_it 3.392 r_mcangle_it 2.024 r_mcbond_it 1.389 r_angle_refined_deg 1.348 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.134 r_dihedral_angle_4_deg 13.665 r_dihedral_angle_3_deg 13.607 r_dihedral_angle_1_deg 5.68 r_scangle_it 4.635 r_scbond_it 3.392 r_mcangle_it 2.024 r_mcbond_it 1.389 r_angle_refined_deg 1.348 r_nbtor_refined 0.295 r_symmetry_metal_ion_refined 0.231 r_symmetry_vdw_refined 0.202 r_nbd_refined 0.199 r_metal_ion_refined 0.182 r_xyhbond_nbd_refined 0.14 r_symmetry_hbond_refined 0.115 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 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_other r_symmetry_vdw_other r_symmetry_hbond_other 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 3847 Nucleic Acid Atoms Solvent Atoms 440 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing