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Crystal structure of NADH-dependent quinuclidinone reductase from agrobacterium tumefaciens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GEG PDB ENTRY 1GEG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 24% PEG3350, 100MM HEPES, 200MM AMMONIUM ACETATE, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.55 α = 90 b = 127.3 β = 110.4 c = 62.48 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 IMAGE PLATE RIGAKU RAXIS VII 2008-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 20 98.1 0.045 20.6 3.5 61144
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 91.4 0.15 7.5 2.9 26076
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1GEG 2 20 58030 3081 99 0.151 0.149 0.191 0.159 RANDOM 15.84
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] 0.75 -0.01 -0.34 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.962 r_dihedral_angle_3_deg 13.417 r_dihedral_angle_4_deg 12.124 r_dihedral_angle_1_deg 6.287 r_scangle_it 3.287 r_scbond_it 2.216 r_angle_refined_deg 1.518 r_mcangle_it 1.175 r_mcbond_it 0.864 r_nbtor_refined 0.287
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.962 r_dihedral_angle_3_deg 13.417 r_dihedral_angle_4_deg 12.124 r_dihedral_angle_1_deg 6.287 r_scangle_it 3.287 r_scbond_it 2.216 r_angle_refined_deg 1.518 r_mcangle_it 1.175 r_mcbond_it 0.864 r_nbtor_refined 0.287 r_symmetry_vdw_refined 0.232 r_symmetry_hbond_refined 0.204 r_nbd_refined 0.188 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.102 r_bond_refined_d 0.019 r_gen_planes_refined 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7596 Nucleic Acid Atoms Solvent Atoms 820 Heterogen Atoms 176
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling