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, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K
Crystal Properties
Matthews coefficientSolvent content
2.5752

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.534α = 90
b = 75.931β = 94.42
c = 186.978γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-10-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBSRF BEAMLINE 3W1A0.978BSRF3W1A

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
12.83093.90.0128.627850168501660.8
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)
2.82.8793.80.4542.225585

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 5PGM2.829.918498984989854293.90.2370.2370.2330.272RANDOM36.2
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]
-0.0924.22-6.937.02
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.2
c_scangle_it2.19
c_mcangle_it1.65
c_scbond_it1.41
c_angle_deg1.3
c_mcbond_it0.95
c_improper_angle_d0.77
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.2
c_scangle_it2.19
c_mcangle_it1.65
c_scbond_it1.41
c_angle_deg1.3
c_mcbond_it0.95
c_improper_angle_d0.77
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms22790
Nucleic Acid Atoms
Solvent Atoms334
Heterogen Atoms162

Software

Software
Software NamePurpose
AMoREphasing
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling