4MY4

Crystal structure of phosphoglycerate mutase from Staphylococcus aureus.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IFY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52980.2M NaCl, Bis-Tris(pH 6.5), 25%(w/v) polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3347.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.206α = 90
b = 81.747β = 90
c = 89.184γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++varimax2013-09-20MSINGLE 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 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
1260.26299.30.08321.773646336463
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1195.70.4650.4650.5110.2061.75.85068

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 REPLACEMENTTHROUGHOUT2IFY219.6936409181899.20.16660.1640.2163RANDOM23.4188
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]
0.241.08-1.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.626
r_dihedral_angle_4_deg19.26
r_dihedral_angle_3_deg17.34
r_dihedral_angle_1_deg6.661
r_angle_refined_deg1.985
r_angle_other_deg0.999
r_chiral_restr0.164
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.626
r_dihedral_angle_4_deg19.26
r_dihedral_angle_3_deg17.34
r_dihedral_angle_1_deg6.661
r_angle_refined_deg1.985
r_angle_other_deg0.999
r_chiral_restr0.164
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3943
Nucleic Acid Atoms
Solvent Atoms372
Heterogen Atoms2

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
XDSdata reduction