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Crystal structure of the human SNP 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 2.82 56.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.556 α = 90 b = 61.239 β = 123.85 c = 113.474 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 2010-04-14 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 2.5 50 99.5 0.065 12.9 3.8 29118 28960 64.5
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 2.5 2.59 99.5 0.641 3 3.8 2763
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 (All) 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 2.5 30 28999 28927 1469 0.286 0.261 0.26 0.2606 0.287 0.2858 RANDOM 66.6636
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] -10.823 -5.015 25.585 -14.762
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.788 c_mcangle_it 2.624 c_scbond_it 1.797 c_mcbond_it 1.483 c_angle_d 1.473 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4383 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