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Crystal Structure of GumK in complex with UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HY7 PDB entry 2HY7 Apo protein GumK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop and soaking of crystals in UDPGlcA 100 mM 8.2 293 0.1 M Tris-HCl, 35% (w/v) PEG 3350, 0.2 M Li2SO4, 0.1 M LiCl, pH 8.2, hanging drop and soaking of crystals in UDPGlcA 100 mM, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.99 69.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.21 α = 90 b = 121.21 β = 90 c = 170.724 γ = 120
Symmetry Space Group P 65 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 MARRESEARCH beam focused by a cilindrically curved mirror 2006-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 1.427 NSLS X12C
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 2.28 104.971 98.5 0.104 0.104 4.3 10.1 33916
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) 2.28 2.4 93.8 0.303 0.303 2.2 9.1
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 ARP/wARP THROUGHOUT PDB entry 2HY7 Apo protein GumK 2.28 104.83 32197 32197 1714 98.51 0.17746 0.17541 0.1747 0.21641 0.2151 RANDOM 21.077
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] 0.22 0.11 0.22 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.795 r_dihedral_angle_4_deg 19.678 r_dihedral_angle_3_deg 13.382 r_dihedral_angle_1_deg 8.549 r_scangle_it 4.371 r_scbond_it 2.812 r_angle_refined_deg 1.682 r_mcangle_it 1.639 r_mcbond_it 1.08 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.795 r_dihedral_angle_4_deg 19.678 r_dihedral_angle_3_deg 13.382 r_dihedral_angle_1_deg 8.549 r_scangle_it 4.371 r_scbond_it 2.812 r_angle_refined_deg 1.682 r_mcangle_it 1.639 r_mcbond_it 1.08 r_nbtor_refined 0.319 r_symmetry_vdw_refined 0.262 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.206 r_symmetry_hbond_refined 0.194 r_chiral_restr 0.105 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2935 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 25
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction ARP/wARP model building