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Crystal structure of human peptidylarginine deiminase 4 in complex with o-F-amidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WDA PDB ENTRY 1WDA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.81 56.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.422 α = 90 b = 60.468 β = 124.43 c = 115.506 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 CCD ADSC QUANTUM 270 2009-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 50 44771
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 1WDA 2.1 20 42464 2254 100 0.22086 0.21928 0.2297 0.2502 0.2628 RANDOM 79.135
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] -3.52 -2.67 2.83 -2.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.774 r_dihedral_angle_3_deg 13.767 r_dihedral_angle_4_deg 13.693 r_dihedral_angle_1_deg 5.551 r_angle_other_deg 3.025 r_angle_refined_deg 0.887 r_scangle_it 0.794 r_mcangle_it 0.485 r_scbond_it 0.467 r_mcbond_it 0.261
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.774 r_dihedral_angle_3_deg 13.767 r_dihedral_angle_4_deg 13.693 r_dihedral_angle_1_deg 5.551 r_angle_other_deg 3.025 r_angle_refined_deg 0.887 r_scangle_it 0.794 r_mcangle_it 0.485 r_scbond_it 0.467 r_mcbond_it 0.261 r_chiral_restr 0.055 r_mcbond_other 0.028 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_gen_planes_other 0.002 r_bond_other_d 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4947 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement