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Cys-Gly dipeptidase GliJ mutant D304A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LX0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M MES pH 6.0, 10% PEG6000
Crystal Properties Matthews coefficient Solvent content 3.38 63.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.33 α = 90 b = 99.33 β = 90 c = 106.88 γ = 120
Symmetry Space Group P 32 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-F 2014-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 2.7 45 99.4 0.073 16.6 6 17088
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 2.7 2.8 99.7 0.453 3.4
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 5LX0 2.7 15 16118 849 98.74 0.18099 0.179 0.1833 0.22007 0.2205 RANDOM 59.275
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] 0.34 0.17 0.34 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.772 r_dihedral_angle_3_deg 16.327 r_dihedral_angle_4_deg 15.075 r_dihedral_angle_1_deg 6.243 r_long_range_B_refined 3.164 r_long_range_B_other 3.164 r_scangle_other 1.947 r_mcangle_other 1.758 r_mcangle_it 1.757 r_angle_refined_deg 1.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.772 r_dihedral_angle_3_deg 16.327 r_dihedral_angle_4_deg 15.075 r_dihedral_angle_1_deg 6.243 r_long_range_B_refined 3.164 r_long_range_B_other 3.164 r_scangle_other 1.947 r_mcangle_other 1.758 r_mcangle_it 1.757 r_angle_refined_deg 1.193 r_scbond_it 1.115 r_scbond_other 1.112 r_mcbond_it 1.021 r_mcbond_other 1.021 r_angle_other_deg 0.945 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 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 3008 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing