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X-ray co-crystal structure of NCGC00685960 / NCATS-SM9335 in NNMT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.15 M DL-Malic acid pH 7.0, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.74 55.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.596 α = 90 b = 91.596 β = 90 c = 213.257 γ = 120
Symmetry Space Group P 32 2 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 PIXEL DECTRIS PILATUS 6M 2019-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9793 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.41 50 99 0.999 16.3 5.4 40333
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.41 2.5 99.1 0.939
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.413 45.798 40287 1922 98.912 0.198 0.1965 0.2007 0.2343 0.2396 70.917
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] -0.107 -0.054 -0.107 0.348
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.789 r_dihedral_angle_6_deg 10.664 r_dihedral_angle_1_deg 6.388 r_dihedral_angle_2_deg 4.205 r_lrange_it 3.571 r_lrange_other 3.561 r_scangle_it 2.174 r_scangle_other 2.174 r_mcangle_it 1.967 r_mcangle_other 1.966
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.789 r_dihedral_angle_6_deg 10.664 r_dihedral_angle_1_deg 6.388 r_dihedral_angle_2_deg 4.205 r_lrange_it 3.571 r_lrange_other 3.561 r_scangle_it 2.174 r_scangle_other 2.174 r_mcangle_it 1.967 r_mcangle_other 1.966 r_scbond_it 1.255 r_scbond_other 1.255 r_mcbond_it 1.139 r_mcbond_other 1.138 r_angle_refined_deg 1.08 r_angle_other_deg 0.345 r_nbd_refined 0.192 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.176 r_symmetry_nbd_refined 0.153 r_nbd_other 0.146 r_xyhbond_nbd_refined 0.109 r_symmetry_xyhbond_nbd_refined 0.081 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.045 r_symmetry_xyhbond_nbd_other 0.042 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6197 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing