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Complex structure of PctV K276R mutant with PMP and 3-dehydroshkimate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZM3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.8 278 PEG 4000, magnesium chloride, MES-Na
Crystal Properties Matthews coefficient Solvent content 2.43 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.93 α = 90 b = 178.93 β = 90 c = 467.899 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 100 CCD ADSC QUANTUM 210r 2014-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 2.4 30 92.1 0.188 7.3 7.3 102961
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 2.4 2.53 92.9 0.685 2.5 6.9
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 4ZM3 2.4 29.98 97822 5134 91.49 0.23999 0.23802 0.2455 0.27756 0.2827 RANDOM 31.005
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] -0.07 -0.07 -0.07 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.608 r_dihedral_angle_4_deg 19.848 r_dihedral_angle_3_deg 15.731 r_dihedral_angle_1_deg 6.188 r_angle_refined_deg 1.475 r_angle_other_deg 1.163 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.608 r_dihedral_angle_4_deg 19.848 r_dihedral_angle_3_deg 15.731 r_dihedral_angle_1_deg 6.188 r_angle_refined_deg 1.475 r_angle_other_deg 1.163 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.006 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18832 Nucleic Acid Atoms Solvent Atoms 767 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction MOSFLM data scaling MOLREP phasing Coot model building