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Crystal structure of the ZP-N1 and ZP-N2 domains of human ZP2 (hZP2-N1N2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5II6 ZP-N1 DOMAIN ENSEMBLE FROM PDB ENTRIES 5II6 AND 8RKE experimental model PDB 8RKE ZP-N1 DOMAIN ENSEMBLE FROM PDB ENTRIES 5II6 AND 8RKE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 10-30% (v/v) MPD, 0.1 M MES pH 6.0 or 0.1 M Na-HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.69 66.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.93 α = 90 b = 86.93 β = 90 c = 178.68 γ = 120
Symmetry Space Group P 31 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 2013-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.95378 ESRF ID23-1
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 3.2 19.9 99.3 0.154 0.163 0.052 1 11.8 9.7 13385 130.16
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 3.2 3.31 99.2 3.808 4.018 1.275 0.34 0.6 9.8
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 ZP-N1 domain ensemble from PDB entries 5II6 and D_1292121897 3.2 19.87 1.34 13368 1320 99.84 0.2402 0.2343 0.2365 0.2926 0.2916 147.8
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 10.2962 f_angle_d 0.6916 f_chiral_restr 0.0574 f_plane_restr 0.0057 f_bond_d 0.0033
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3128 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 84
Software Software Software Name Purpose MxCuBE data collection XDS data reduction XSCALE data scaling PHASER phasing PHENIX model building Coot model building PHENIX refinement