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The crystal structure of EndoV from E.coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NSP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 26% PEG 3350, 0.05M sodium fluoride, 0.1M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.27 45.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.892 α = 90 b = 84.783 β = 90 c = 91.507 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 180 CCD OXFORD ONYX CCD Onyx 2014-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OXFORD DIFFRACTION ENHANCE ULTRA 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.4 62.2 99.5 0.157 9.5 4.7 17499
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 99.9 0.669 2.5 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4NSP 2.4 62.19 16581 887 99.23 0.19791 0.19484 0.1997 0.25512 0.2591 RANDOM 27.212
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] -0.54 -0.42 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.427 r_dihedral_angle_3_deg 19.203 r_dihedral_angle_4_deg 19.03 r_dihedral_angle_1_deg 6.393 r_long_range_B_refined 5.49 r_long_range_B_other 5.434 r_scangle_other 3.242 r_mcangle_it 2.663 r_mcangle_other 2.662 r_scbond_it 1.948
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.427 r_dihedral_angle_3_deg 19.203 r_dihedral_angle_4_deg 19.03 r_dihedral_angle_1_deg 6.393 r_long_range_B_refined 5.49 r_long_range_B_other 5.434 r_scangle_other 3.242 r_mcangle_it 2.663 r_mcangle_other 2.662 r_scbond_it 1.948 r_scbond_other 1.948 r_angle_refined_deg 1.666 r_mcbond_it 1.626 r_mcbond_other 1.624 r_angle_other_deg 0.895 r_chiral_restr 0.084 r_bond_other_d 0.017 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3242 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction SCALA data scaling PHASER phasing