☰ Navigation Tabs
Crystal structure of a hypothetical protein Rv3716c from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YBX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 5.5 293 20mM Sodium phosphate pH 5.5 0.1M Cadmium chloride 0.1M Magnesium chloride 0.1M Nickel chloride 24% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.31 41.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.11 α = 90 b = 183.75 β = 90 c = 37.25 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2017-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 37.25 99.9 0.08 0.031 0.086 0.025 0.997 24.6 13.7 9968 14.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 100 0.227 0.239 0.244 0.091 0.985 12.1 13.5
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 1YBX 1.9 32 9467 464 99.63 0.17423 0.17215 0.1863 0.21594 0.205 RANDOM 31.881
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] -0.31 1.57 -1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.71 r_dihedral_angle_3_deg 15.229 r_dihedral_angle_4_deg 14.011 r_long_range_B_refined 9.208 r_long_range_B_other 9.108 r_dihedral_angle_1_deg 8.188 r_scangle_other 7.057 r_scbond_other 4.906 r_scbond_it 4.902 r_mcangle_other 4.777
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.71 r_dihedral_angle_3_deg 15.229 r_dihedral_angle_4_deg 14.011 r_long_range_B_refined 9.208 r_long_range_B_other 9.108 r_dihedral_angle_1_deg 8.188 r_scangle_other 7.057 r_scbond_other 4.906 r_scbond_it 4.902 r_mcangle_other 4.777 r_mcangle_it 4.774 r_mcbond_it 3.439 r_mcbond_other 3.407 r_angle_refined_deg 2.282 r_angle_other_deg 1.169 r_chiral_restr 0.159 r_bond_refined_d 0.024 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 482 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing