1M3U

Crystal Structure of Ketopantoate Hydroxymethyltransferase complexed the Product Ketopantoate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherInitial 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
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.8277PEG 8000, sodium chloride, sodium acetate, sodium citrate buffer, pH 6.8, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3848.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.074α = 90
b = 157.17β = 97.44
c = 100.181γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-2mirror1999-08-26MMAD
21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97927, 0.9393, 0.979APS19-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.87594.20.0830.08312.94.52290862290861
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)RedundancyNumber Unique Reflections (All)
11.81.9750.5270.5272.43.526449

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUTInitial 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)1.8100-1-1224262224262481294.120.158440.152760.151930.19258random22.888
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]
0.47-0.370.27-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg13.928
r_dihedral_angle_1_deg5.983
r_scangle_it3.715
r_scbond_it2.31
r_angle_refined_deg1.548
r_mcangle_it1.403
r_angle_other_deg0.88
r_mcbond_it0.791
r_symmetry_vdw_other0.255
r_nbd_other0.237
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg13.928
r_dihedral_angle_1_deg5.983
r_scangle_it3.715
r_scbond_it2.31
r_angle_refined_deg1.548
r_mcangle_it1.403
r_angle_other_deg0.88
r_mcbond_it0.791
r_symmetry_vdw_other0.255
r_nbd_other0.237
r_symmetry_hbond_refined0.224
r_nbd_refined0.212
r_xyhbond_nbd_refined0.182
r_symmetry_vdw_refined0.128
r_chiral_restr0.092
r_nbtor_other0.085
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms19602
Nucleic Acid Atoms
Solvent Atoms2776
Heterogen Atoms110

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
SHARPphasing
REFMACrefinement
CCP4data scaling