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Crystal structure of LysM domain from Volvox carteri chitinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PXV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Sodium citrate tribasic dihydrate,
20 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2 34.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.13 α = 90 b = 29.13 β = 90 c = 94.257 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 95 PIXEL DECTRIS PILATUS3 6M 2014-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.2 50 99.5 73 23.5 13481
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22
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 4PXV 1.2 27.83 12739 688 99.64 0.14073 0.13871 0.1467 0.17959 0.1887 RANDOM 9.587
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] 0.1 0.1 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.655 r_dihedral_angle_3_deg 15.04 r_sphericity_free 14.866 r_dihedral_angle_4_deg 13.457 r_rigid_bond_restr 8.858 r_sphericity_bonded 6.963 r_dihedral_angle_1_deg 4.578 r_long_range_B_refined 3.903 r_long_range_B_other 3.9 r_scangle_other 3.362
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.655 r_dihedral_angle_3_deg 15.04 r_sphericity_free 14.866 r_dihedral_angle_4_deg 13.457 r_rigid_bond_restr 8.858 r_sphericity_bonded 6.963 r_dihedral_angle_1_deg 4.578 r_long_range_B_refined 3.903 r_long_range_B_other 3.9 r_scangle_other 3.362 r_scbond_it 3.04 r_scbond_other 3.035 r_angle_other_deg 2.852 r_angle_refined_deg 1.999 r_mcangle_other 1.582 r_mcbond_it 1.42 r_mcangle_it 1.408 r_mcbond_other 1.163 r_chiral_restr 0.136 r_bond_refined_d 0.026 r_gen_planes_other 0.02 r_gen_planes_refined 0.01 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 369 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing