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GlnK2 from Archaeoglobus fulgidus, ATP complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NCP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 ammonium phosphate, Tris-HCl, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.89 57.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.663 α = 90 b = 121.663 β = 90 c = 124.582 γ = 90
Symmetry Space Group I 4 2 2
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 MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 1.00 EMBL/DESY, HAMBURG X12
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.24 39.3 99.2 0.1082 0.1082 9.93 6.54 131297 130294 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.24 1.34 96.5 0.5893 0.5893 2.7 4.4
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 (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 3NCP 1.24 39.3 130294 123582 6547 99.41 0.16968 0.16768 0.1675 0.20837 0.2083 RANDOM 25.363
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] 0.02 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.03 r_dihedral_angle_4_deg 18.604 r_dihedral_angle_3_deg 14.642 r_scangle_it 9.847 r_scbond_it 6.543 r_dihedral_angle_1_deg 6.202 r_mcangle_it 4.432 r_rigid_bond_restr 3.481 r_mcbond_it 3.034 r_angle_refined_deg 2.403
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.03 r_dihedral_angle_4_deg 18.604 r_dihedral_angle_3_deg 14.642 r_scangle_it 9.847 r_scbond_it 6.543 r_dihedral_angle_1_deg 6.202 r_mcangle_it 4.432 r_rigid_bond_restr 3.481 r_mcbond_it 3.034 r_angle_refined_deg 2.403 r_chiral_restr 0.157 r_bond_refined_d 0.027 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2618 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 119
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling