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Glutaminase domain of glucosamine 6-phosphate synthase complexed with glutamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GPH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 0.1 M cacodylate, 1 M sodium acetate, 20% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.36 47.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.38 α = 90 b = 82.52 β = 90 c = 86.05 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 295 IMAGE PLATE MARRESEARCH MIRROR 1993-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.99 EMBL/DESY, HAMBURG X11
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 1.8 24 99.9 0.062 14.4 5.2 47043 -3 18.3
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) 1.8 1.82 97.1 0.283 3 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT none used 1GPH 1.8 20 47018 47018 99.8 0.1611 0.1611 0.161 0.1624 25.5
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] 0.98 -0.64 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.769 r_scangle_it 12.577 r_dihedral_angle_1_deg 11.454 r_scbond_it 9.906 r_mcangle_it 6.945 r_mcbond_it 4.496 r_angle_refined_deg 1.728 r_nbtor_refined 0.326 r_symmetry_vdw_refined 0.31 r_nbd_refined 0.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.769 r_scangle_it 12.577 r_dihedral_angle_1_deg 11.454 r_scbond_it 9.906 r_mcangle_it 6.945 r_mcbond_it 4.496 r_angle_refined_deg 1.728 r_nbtor_refined 0.326 r_symmetry_vdw_refined 0.31 r_nbd_refined 0.239 r_symmetry_hbond_refined 0.139 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.121 r_bond_refined_d 0.015 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3746 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 26
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement