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Crystal structure of GltPh in complex with L-aspartate and sodium ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XFH PDB ENTRY 1xfh
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.66 73.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.473 α = 90 b = 115.473 β = 90 c = 324.227 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.978 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.29 100 9.4 17.1 5.2 25514 25514
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.29 3.72 30.2 34.8 17.7 2.1
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 PDB ENTRY 1xfh 3.29 100 25514 1261 69.21 0.265 0.263 0.2504 0.286 0.2558 RANDOM 134.632
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] 2.85 1.43 2.85 -4.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.783 r_dihedral_angle_4_deg 24.277 r_dihedral_angle_3_deg 22.508 r_dihedral_angle_1_deg 7.168 r_mcangle_it 1.855 r_angle_refined_deg 1.687 r_scangle_it 1.142 r_mcbond_it 1.043 r_scbond_it 0.707 r_nbtor_refined 0.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.783 r_dihedral_angle_4_deg 24.277 r_dihedral_angle_3_deg 22.508 r_dihedral_angle_1_deg 7.168 r_mcangle_it 1.855 r_angle_refined_deg 1.687 r_scangle_it 1.142 r_mcbond_it 1.043 r_scbond_it 0.707 r_nbtor_refined 0.332 r_metal_ion_refined 0.322 r_symmetry_vdw_refined 0.273 r_nbd_refined 0.25 r_xyhbond_nbd_refined 0.198 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8509 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction HKL-2000 data scaling