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The crystal structure of Xanthomonas albilineans N5, N10-methylenetetrahydrofolate dehydrogenase-cyclohydrolase (FolD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B0A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 291 0.15 M malic acid, 20% PEG 3350, 0.1 M sodium cacodylate pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.5 50.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.295 α = 90 b = 76.404 β = 90 c = 66.641 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M 2014-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.45864 LNLS W01B-MX2
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 2.11 66.64 99.2 0.1 1.45 2 36804
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.11 2.17 94.6 0.97 0.47 1.5 4 2845
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 1B0A 2.11 66.64 35007 1812 99.25 0.19358 0.19116 0.1981 0.24054 0.2437 RANDOM 42.668
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] -0.04 1.42 -1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.798 r_dihedral_angle_4_deg 14.759 r_dihedral_angle_3_deg 14.599 r_long_range_B_refined 7.021 r_long_range_B_other 7.013 r_dihedral_angle_1_deg 6.133 r_scangle_other 4.07 r_mcangle_it 3.051 r_mcangle_other 3.051 r_scbond_it 2.551
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.798 r_dihedral_angle_4_deg 14.759 r_dihedral_angle_3_deg 14.599 r_long_range_B_refined 7.021 r_long_range_B_other 7.013 r_dihedral_angle_1_deg 6.133 r_scangle_other 4.07 r_mcangle_it 3.051 r_mcangle_other 3.051 r_scbond_it 2.551 r_scbond_other 2.55 r_angle_refined_deg 2.148 r_mcbond_it 1.916 r_mcbond_other 1.916 r_angle_other_deg 1.148 r_chiral_restr 0.127 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4149 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing