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Structure of E. coli DHDPS mutant Y107W
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YXC PDB ENTRY 1YXC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10 284 1.8M K2HPO4, 6% (w/v) N-octyl-beta-R-glucopyranoside , pH 10, VAPOR DIFFUSION, HANGING DROP, temperature 284K
Crystal Properties Matthews coefficient Solvent content 3.73 66.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.196 α = 90 b = 121.196 β = 90 c = 110.565 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE RIGAKU RAXIS IV++ 2007-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 39.67 99.3 0.095 8.2 3.99 63201 3 38.4
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 2.07 100 0.432 2.8 3.98 6275
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1YXC 2.2 32.22 45136 2388 100 0.18586 0.18303 0.24098 0.2201 RANDOM 31.218
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] -0.13 -0.06 -0.13 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.822 r_dihedral_angle_4_deg 17.433 r_dihedral_angle_3_deg 15.69 r_dihedral_angle_1_deg 6.491 r_scangle_it 4.56 r_scbond_it 2.873 r_angle_refined_deg 1.826 r_mcangle_it 1.647 r_mcbond_it 0.892 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.822 r_dihedral_angle_4_deg 17.433 r_dihedral_angle_3_deg 15.69 r_dihedral_angle_1_deg 6.491 r_scangle_it 4.56 r_scbond_it 2.873 r_angle_refined_deg 1.826 r_mcangle_it 1.647 r_mcbond_it 0.892 r_nbtor_refined 0.294 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.184 r_symmetry_vdw_refined 0.182 r_metal_ion_refined 0.149 r_chiral_restr 0.116 r_symmetry_hbond_refined 0.078 r_bond_refined_d 0.02 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_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 4369 Nucleic Acid Atoms Solvent Atoms 448 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling AMoRE phasing