3K73

Crystal Structure of Phosphate bound Holo Glyceraldehyde-3-phosphate dehydrogenase 1 from MRSA252 at 2.5 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H48 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52980.1M Tris-HCl pH 8.5, 25% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1342.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.2α = 90
b = 104.851β = 107.57
c = 90.604γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2009-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.586.3899.80.0858.13.024193746.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5999.70.3762.52.864163

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3H482.519.1441927211599.530.1790.1770.224RANDOM60.342
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]
2.161.43-1.510.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.676
r_dihedral_angle_4_deg22.546
r_dihedral_angle_3_deg15.463
r_scangle_it6.93
r_dihedral_angle_1_deg6.546
r_scbond_it4.063
r_angle_refined_deg1.553
r_mcangle_it1.394
r_mcbond_it0.636
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.676
r_dihedral_angle_4_deg22.546
r_dihedral_angle_3_deg15.463
r_scangle_it6.93
r_dihedral_angle_1_deg6.546
r_scbond_it4.063
r_angle_refined_deg1.553
r_mcangle_it1.394
r_mcbond_it0.636
r_chiral_restr0.095
r_bond_refined_d0.015
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10184
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms216

Software

Software
Software NamePurpose
d*TREKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction