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X-Ray Structure of imidazoleglycerol-phosphate dehydratase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RHY PDB entry 1RHY
Crystallization Crystal Properties Matthews coefficient Solvent content 3.21 61.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.949 α = 90 b = 157.949 β = 90 c = 479.965 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray IMAGE PLATE MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 3 50 98.3 0.097 11.7 3.7 88754
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 1RHY 3 20 83229 4375 98.33 0.24262 0.24034 0.2277 0.28633 0.2273 RANDOM 16.845
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] 0.48 0.24 0.48 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.905 r_angle_refined_deg 1.277 r_angle_other_deg 0.764 r_symmetry_vdw_other 0.248 r_nbd_other 0.215 r_nbd_refined 0.19 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.157 r_symmetry_vdw_refined 0.111 r_nbtor_other 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.905 r_angle_refined_deg 1.277 r_angle_other_deg 0.764 r_symmetry_vdw_other 0.248 r_nbd_other 0.215 r_nbd_refined 0.19 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.157 r_symmetry_vdw_refined 0.111 r_nbtor_other 0.085 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22176 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing