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Crystal Structure of Ketopantoate Hydroxymethyltransferase complexed the Product Ketopantoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Initial C-alpha trace obtained from 3.0 A selenomethionine MAD-phased maps of a different crystal form: P21, cell=(87.8,155.4,209.9,90,99.3,90)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.8 277 PEG 8000, sodium chloride, sodium acetate, sodium citrate buffer, pH 6.8, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.38 48.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.074 α = 90 b = 157.17 β = 97.44 c = 100.181 γ = 90
Symmetry Space Group P 1 21 1
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 SBC-2 mirror 1999-08-26 M MAD 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97927, 0.9393, 0.979 APS 19-ID
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 1.8 75 94.2 0.083 0.083 12.9 4.5 229086 229086 1
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) 1 1.8 1.9 75 0.527 0.527 2.4 3.5 26449
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 MAD THROUGHOUT Initial C-alpha trace obtained from 3.0 A selenomethionine MAD-phased maps of a different crystal form: P21, cell=(87.8,155.4,209.9,90,99.3,90) 1.8 100 -1 -1 224262 224262 4812 94.12 0.15844 0.15276 0.15193 0.1639 0.19258 0.202 random 22.888
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] 0.47 -0.37 0.27 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.928 r_dihedral_angle_1_deg 5.983 r_scangle_it 3.715 r_scbond_it 2.31 r_angle_refined_deg 1.548 r_mcangle_it 1.403 r_angle_other_deg 0.88 r_mcbond_it 0.791 r_symmetry_vdw_other 0.255 r_nbd_other 0.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.928 r_dihedral_angle_1_deg 5.983 r_scangle_it 3.715 r_scbond_it 2.31 r_angle_refined_deg 1.548 r_mcangle_it 1.403 r_angle_other_deg 0.88 r_mcbond_it 0.791 r_symmetry_vdw_other 0.255 r_nbd_other 0.237 r_symmetry_hbond_refined 0.224 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.182 r_symmetry_vdw_refined 0.128 r_chiral_restr 0.092 r_nbtor_other 0.085 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19602 Nucleic Acid Atoms Solvent Atoms 2776 Heterogen Atoms 110
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling SnB phasing SHARP phasing REFMAC refinement CCP4 data scaling