☰ Navigation Tabs
Crystal Structure of D86N-GzmM Complexed with Its Optimal Synthesized Substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZGC PDB ENTRY 2ZGC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 289 0.1M Bicine, 0.2M Li2SO4, 21% PEG3350, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.35 63.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.487 α = 90 b = 74.487 β = 90 c = 112.689 γ = 120
Symmetry Space Group P 31 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 93 IMAGE PLATE RIGAKU RAXIS IV 2007-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.3 50 99.4 0.051 36.1 5.8 16708 16608
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.35 99.4 0.399 3.38 4.9 1080
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 PDB ENTRY 2ZGC 2.3 26.45 15700 832 99.52 0.24226 0.23994 0.2373 0.28779 0.2858 RANDOM 49.105
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] -0.26 -0.13 -0.26 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.499 r_dihedral_angle_4_deg 18.954 r_dihedral_angle_3_deg 18.111 r_dihedral_angle_1_deg 7.625 r_scangle_it 3.714 r_scbond_it 2.543 r_angle_refined_deg 1.859 r_mcangle_it 1.533 r_mcbond_it 0.944 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.499 r_dihedral_angle_4_deg 18.954 r_dihedral_angle_3_deg 18.111 r_dihedral_angle_1_deg 7.625 r_scangle_it 3.714 r_scbond_it 2.543 r_angle_refined_deg 1.859 r_mcangle_it 1.533 r_mcbond_it 0.944 r_nbtor_refined 0.314 r_nbd_refined 0.246 r_symmetry_vdw_refined 0.207 r_symmetry_hbond_refined 0.167 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.124 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1796 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing