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Crystal structure of NRMT1 in complex with SPKRIA peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EX4 pdbid 2ex4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 26% PEG3350, 16% tacsimate
Crystal Properties Matthews coefficient Solvent content 3.05 59.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.259 α = 90 b = 107.259 β = 90 c = 205.416 γ = 120
Symmetry Space Group P 65 2 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 CCD ADSC QUANTUM 315 2015-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.6 50.01 100 0.134 0.137 0.029 0.999 21.7 21.7 92380
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 100 1.213 1.241 0.265 0.869 3.2 21.8 4488
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 pdbid 2ex4 1.65 47.54 80997 3324 99.99 0.1517 0.1507 0.1647 0.1759 0.1863 THIN SHELLS (SFTOOLS) 16.708
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 0.02 0.04 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.74 r_dihedral_angle_4_deg 18.522 r_dihedral_angle_3_deg 11.088 r_dihedral_angle_1_deg 6.182 r_angle_refined_deg 1.815 r_angle_other_deg 1.04 r_mcangle_it 0.878 r_mcbond_it 0.517 r_mcbond_other 0.512 r_chiral_restr 0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.74 r_dihedral_angle_4_deg 18.522 r_dihedral_angle_3_deg 11.088 r_dihedral_angle_1_deg 6.182 r_angle_refined_deg 1.815 r_angle_other_deg 1.04 r_mcangle_it 0.878 r_mcbond_it 0.517 r_mcbond_other 0.512 r_chiral_restr 0.119 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3652 Nucleic Acid Atoms Solvent Atoms 436 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction