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Crystal structure of L. lactis dihydroorotate dehydrogense A in complex with 3,4-dihydroxybenzoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OVD PDB ENTRY 1OVD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 17 MG/ML PROTEIN AND 2.6 MM 3, 4-DIOHB HANGING DROPS 2 MICROLITERS OF PROTEIN AND 2 MICROLITERS RESERVOIR: 30 % PEG 6000, 1 MM DTT, 0.2 M SODIUM ACETATE AND 0.1 M TRIS-HCL PH 8.5
Crystal Properties Matthews coefficient Solvent content 2.62 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.588 α = 90 b = 108.16 β = 104.06 c = 66.222 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 120 IMAGE PLATE MARRESEEARCH MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
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 2.3 25 90.6 0.06 22.9 5.7 32557 -3 26
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 2.3 2.32 62.8 0.23 5.6
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 1OVD 2.3 25 27913 1526 90.6 0.189 0.186 0.1895 0.241 0.2417 RANDOM 36.13
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] 6.63 -0.68 -4.28 -2.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.047 r_scangle_it 3.778 r_scbond_it 2.294 r_angle_refined_deg 1.687 r_mcangle_it 1.505 r_angle_other_deg 0.925 r_mcbond_it 0.809 r_nbd_other 0.234 r_nbd_refined 0.216 r_symmetry_vdw_other 0.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.047 r_scangle_it 3.778 r_scbond_it 2.294 r_angle_refined_deg 1.687 r_mcangle_it 1.505 r_angle_other_deg 0.925 r_mcbond_it 0.809 r_nbd_other 0.234 r_nbd_refined 0.216 r_symmetry_vdw_other 0.215 r_symmetry_vdw_refined 0.184 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.1 r_nbtor_other 0.088 r_symmetry_hbond_refined 0.066 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_gen_planes_other 0.008 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined 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 4818 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling