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Crystal structure of Msmeg3575 in complex with ammeline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XKO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 290 0.2 M magnesium acetate tetrahydrate, 0.1 M TRis HCl pH 6.4 and 20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.47 50.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.679 α = 90 b = 61.392 β = 89.95 c = 109.406 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 MARMOSAIC 225 mm CCD 2016-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.98 ESRF BM14
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 2.68 109.41 99.1 0.094 12.9 4.1 19362
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.68 2.75
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 5XKO 2.7 109.41 17737 832 95.07 0.19567 0.19307 0.1972 0.25327 0.2538 RANDOM 45.1
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] -0.03 -0.05 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.365 r_dihedral_angle_4_deg 19.169 r_dihedral_angle_3_deg 15.372 r_long_range_B_refined 7.72 r_long_range_B_other 7.712 r_dihedral_angle_1_deg 5.726 r_scangle_other 5.246 r_mcangle_it 4.848 r_mcangle_other 4.848 r_scbond_it 3.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.365 r_dihedral_angle_4_deg 19.169 r_dihedral_angle_3_deg 15.372 r_long_range_B_refined 7.72 r_long_range_B_other 7.712 r_dihedral_angle_1_deg 5.726 r_scangle_other 5.246 r_mcangle_it 4.848 r_mcangle_other 4.848 r_scbond_it 3.293 r_scbond_other 3.292 r_mcbond_it 3.124 r_mcbond_other 3.124 r_angle_refined_deg 1.452 r_angle_other_deg 1.421 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_gen_planes_other 0.007 r_bond_other_d 0.006 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 4605 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing