☰ Navigation Tabs
Human GMP synthetase - glutaminase domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GPM PDB ENTRY 1GPM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 0.2 M AMMONIUM ACETATE 0.1 M BIS-TRIS PH 5.5 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.38 40.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.68 α = 90 b = 120.88 β = 106.43 c = 47.32 γ = 90
Symmetry Space Group P 1 21 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 CCD MARRESEARCH MIRRORS 2007-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 2.4 20 96 0.14 11.52 4.13 14466 2
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 2.4 2.5 92.4 0.56 2.96 3.88
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 1GPM 2.4 19.77 13703 733 96.1 0.206 0.203 0.2019 0.261 0.261 RANDOM 16.35
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] 0.06 0.61 -0.37 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.269 r_dihedral_angle_4_deg 21.629 r_dihedral_angle_3_deg 16.053 r_dihedral_angle_1_deg 5.997 r_scangle_it 2.55 r_scbond_it 1.516 r_angle_refined_deg 1.227 r_mcangle_it 0.954 r_mcbond_it 0.55 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.269 r_dihedral_angle_4_deg 21.629 r_dihedral_angle_3_deg 16.053 r_dihedral_angle_1_deg 5.997 r_scangle_it 2.55 r_scbond_it 1.516 r_angle_refined_deg 1.227 r_mcangle_it 0.954 r_mcbond_it 0.55 r_nbtor_refined 0.302 r_nbd_refined 0.186 r_symmetry_vdw_refined 0.184 r_xyhbond_nbd_refined 0.172 r_symmetry_hbond_refined 0.169 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2837 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing