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Lactobacillus brevis CGMCC 1306 Glutamate decarboxylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XEY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 287 10% W/V PEG 2000 MME, 100mM Sodium Acetate/Acetic acid, 200mM Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 2.52 51.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.333 α = 90 b = 170.129 β = 90 c = 164.567 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 82 CCD ADSC QUANTUM 315r 2016-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL18U 0.97851 NFPSS BL18U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.15 50.01 100 0.176 0.93 10.88 6.7 85974
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.23 100 0.7 0.84 6.7
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 1xey 2.16 48.543 81517 4290 99.32 0.18911 0.18694 0.1949 0.23005 0.2354 RANDOM 31.556
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 -0.35 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.449 r_dihedral_angle_4_deg 23.705 r_dihedral_angle_3_deg 17.737 r_long_range_B_refined 6.988 r_long_range_B_other 6.988 r_dihedral_angle_1_deg 6.618 r_scangle_other 5.56 r_mcangle_other 4.254 r_mcangle_it 4.253 r_scbond_it 3.593
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.449 r_dihedral_angle_4_deg 23.705 r_dihedral_angle_3_deg 17.737 r_long_range_B_refined 6.988 r_long_range_B_other 6.988 r_dihedral_angle_1_deg 6.618 r_scangle_other 5.56 r_mcangle_other 4.254 r_mcangle_it 4.253 r_scbond_it 3.593 r_scbond_other 3.592 r_mcbond_it 2.869 r_mcbond_other 2.867 r_angle_refined_deg 1.983 r_angle_other_deg 1.188 r_chiral_restr 0.142 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 10498 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection SCALEPACK data scaling PHASER phasing MERLOT data processing