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Structure of wt Porphyromonas gingivalis peptidylarginine deiminase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 22% PEG3350, 0.1M BIS-TRIS PH 5.5, 0.1M LITHIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 2.43 49.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.86 α = 90 b = 84.66 β = 92.5 c = 55.66 γ = 90
Symmetry Space Group C 1 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 2014-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.46 65.08 97.9 0.04 14.3 3.4 79913 1
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 1.46 1.5 95 0.49 2.2 3.2
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 (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 1.46 65.08 75992 3920 97.77 0.12952 0.12822 0.1397 0.15402 0.1609 RANDOM 19.083
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] -0.59 0.04 1.08 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.511 r_sphericity_free 26.354 r_dihedral_angle_4_deg 11.531 r_dihedral_angle_3_deg 10.451 r_sphericity_bonded 8.634 r_dihedral_angle_1_deg 5.951 r_scbond_it 2.138 r_mcangle_it 1.41 r_angle_refined_deg 1.27 r_mcbond_it 1.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.511 r_sphericity_free 26.354 r_dihedral_angle_4_deg 11.531 r_dihedral_angle_3_deg 10.451 r_sphericity_bonded 8.634 r_dihedral_angle_1_deg 5.951 r_scbond_it 2.138 r_mcangle_it 1.41 r_angle_refined_deg 1.27 r_mcbond_it 1.047 r_mcbond_other 1.047 r_rigid_bond_restr 0.958 r_angle_other_deg 0.89 r_chiral_restr 0.078 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3289 Nucleic Acid Atoms Solvent Atoms 481 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling Rosetta phasing