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Crystal structure of the human wild-type PAD4 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WD8 PDB ENTRY 1WD8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 imidazole, lithium sulfate, PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.81 56.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.254 α = 90 b = 61.064 β = 123.74 c = 113.569 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 RAYONIX MX225HE 2010-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.7 50 99.7 0.065 13.9 3.8 23035 22962 82.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.75 100 0.751 2.3 3.8 1137
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1WD8 2.7 30 23013 22922 1179 99.6 0.247 0.246 0.2461 0.293 0.2891 RANDOM 77.6613
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] -6.632 -7.149 28.358 -21.726
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.2 c_scangle_it 2.741 c_mcangle_it 2.618 c_scbond_it 1.741 c_angle_d 1.542 c_mcbond_it 1.485 c_improper_angle_d 1.15 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4407 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose BSS data collection PHASER phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling