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Structure of the dihydrofolate reductase (folA) from Coxiella burnetii in complex with methotrexate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unliganded CBU_1993
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 100 mM HEPES, pH 7.5
25% PEG 6000 , VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.24 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.25 α = 90 b = 37.193 β = 107.66 c = 53.003 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 100 CCD MAR CCD 165 mm 2010-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.979 NSLS X4C
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 2.3 100 85.9 0.047 19 3.4 8329 7154 -3
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 2.3 2.34 50 0.186 3.5 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 Unliganded CBU_1993 2.3 25.73 8317 6776 366 85.87 0.2181 0.21563 0.2145 0.2659 0.2622 RANDOM 73.938
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] 6.74 1.25 -1.48 -4.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.673 r_dihedral_angle_3_deg 14.606 r_dihedral_angle_4_deg 13.149 r_dihedral_angle_1_deg 5.424 r_scangle_it 1.46 r_angle_refined_deg 1.328 r_angle_other_deg 0.893 r_scbond_it 0.879 r_mcangle_it 0.514 r_mcbond_it 0.259
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.673 r_dihedral_angle_3_deg 14.606 r_dihedral_angle_4_deg 13.149 r_dihedral_angle_1_deg 5.424 r_scangle_it 1.46 r_angle_refined_deg 1.328 r_angle_other_deg 0.893 r_scbond_it 0.879 r_mcangle_it 0.514 r_mcbond_it 0.259 r_chiral_restr 0.067 r_mcbond_other 0.051 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1228 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 81
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling