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Crystal structure of S202G mutant of human SYT-5 C2A domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H4Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 287 0.1M calcium acetate, 0.1M sodium acetate pH 4.0, 10%(w/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 3.6 71.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.005 α = 90 b = 118.656 β = 90 c = 109.464 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 CCD ADSC QUANTUM 315r 2016-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97916 SSRF BL17U
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 3 50 99.9 0.167 15.6 6.4 9990
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 3 3.05 100 0.837 3.1
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 5H4Y 3.01 50 9496 474 98.74 0.20254 0.19997 0.196 0.25745 0.2467 RANDOM 22.754
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] -1.62 3.78 -2.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.763 r_dihedral_angle_4_deg 20.763 r_dihedral_angle_3_deg 20.259 r_dihedral_angle_1_deg 7.007 r_scangle_it 2.044 r_angle_refined_deg 1.331 r_mcangle_it 1.264 r_scbond_it 1.126 r_angle_other_deg 0.834 r_mcbond_it 0.673
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.763 r_dihedral_angle_4_deg 20.763 r_dihedral_angle_3_deg 20.259 r_dihedral_angle_1_deg 7.007 r_scangle_it 2.044 r_angle_refined_deg 1.331 r_mcangle_it 1.264 r_scbond_it 1.126 r_angle_other_deg 0.834 r_mcbond_it 0.673 r_chiral_restr 0.074 r_mcbond_other 0.058 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1992 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing