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Crystal structure of NLPPya P41A, D44N, N48E mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GNZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.3 M MgCl2, 0.1 M Tris/HCl pH 9, 10 % (v/v) glycerol, 5 % (v/v) methanol, 22 % (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.38 48.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.391 α = 90 b = 87.391 β = 90 c = 115.967 γ = 90
Symmetry Space Group P 41 21 2
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 2M a vertical collimating mirror, a double-crystal Si(111) monochromator, a bendable focussing mirror 2015-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.94 42.284 100 0.225 0.234 0.991 9.38 13.024 33415 18.64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2.06 100 0.715 0.746 0.925 3.52 12.198
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 THROUGHOUT 3GNZ 1.95 42.284 1.36 33411 2000 99.99 0.1718 0.1696 0.1705 0.2068 0.2076 17.2826
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 5.102 f_angle_d 0.759 f_chiral_restr 0.051 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3168 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 3
Software Software Software Name Purpose XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction