1YFK

Crystal structure of human B type phosphoglycerate mutase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5PGMPDB ENTRY 5PGM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.7297PEG4000, iso-Propanol, tri-Sodium Citrate dehydrate, (NH4)2SO4, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.5752

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.861α = 90
b = 65.745β = 94.36
c = 124.812γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-03-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBSRF BEAMLINE 3W1A1.0BSRF3W1A

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
12.73094.70.129179811798124.4
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)
2.72.7694.40.436

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 5PGM2.729.07171051710567189.50.2180.2160.2160.255RANDOM30.6
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]
17.0112.34-1.68-15.34
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.2
c_angle_deg1.3
c_improper_angle_d0.83
c_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3801
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms27

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing