☰ Navigation Tabs
Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with IMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K7K PDB CODE 1K7K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 20% PEG3350, 200 mM Mg Acetate, cryoprotected with 7% each of glycerol, sucrose and ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.64 53.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.941 α = 90 b = 77.941 β = 90 c = 81.073 γ = 90
Symmetry Space Group P 43 21 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 IMAGE PLATE RIGAKU RAXIS IV Osmic Mirrors 2006-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 2.02 50 99.9 0.057 37.5 4.9 31924 31488 30.6
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 2.02 2.09 99.6 0.476 5.5 4.7 3168
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 (All) 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 CODE 1K7K 2.02 32.03 16119 860 99.94 0.19506 0.19506 0.19224 0.193 0.25346 0.2559 RANDOM 32.283
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 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.935 r_dihedral_angle_4_deg 21.644 r_dihedral_angle_3_deg 14.233 r_dihedral_angle_1_deg 7.032 r_scangle_it 5.629 r_scbond_it 3.814 r_mcangle_it 2.298 r_angle_refined_deg 2.236 r_mcbond_it 1.517 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.935 r_dihedral_angle_4_deg 21.644 r_dihedral_angle_3_deg 14.233 r_dihedral_angle_1_deg 7.032 r_scangle_it 5.629 r_scbond_it 3.814 r_mcangle_it 2.298 r_angle_refined_deg 2.236 r_mcbond_it 1.517 r_nbtor_refined 0.312 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.229 r_chiral_restr 0.163 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.112 r_bond_refined_d 0.026 r_gen_planes_refined 0.009 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 1559 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing