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Crystal structure of free human Scribble PDZ1 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W4F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.1M Citric acid pH 3.5, 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.93 36.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.108 α = 90 b = 42.824 β = 90 c = 91.234 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 CMOS RDI CMOS_8M 2016-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 0.976251 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.6 45.62 97.8 0.065 0.077 0.03 0.999 18.5 6.2 10237
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 87.4 0.547 0.683 0.339 0.751 1.8 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2W4F 1.6 45.617 1.35 10209 542 97.67 0.1731 0.171 0.1733 0.2103 0.2137
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.833 f_angle_d 0.994 f_chiral_restr 0.064 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 679 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection REFMAC refinement ARP/wARP model building Coot model building Aimless data scaling XDS data reduction SCALA data scaling PHASER phasing