5HPG

STRUCTURE AND LIGAND DETERMINANTS OF THE RECOMBINANT KRINGLE 5 DOMAIN OF HUMAN PLASMINOGEN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PKRPDB ENTRY 1PKR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1724% (W/V) PEG 8000, 0.1 M NA-HEPES, PH 7.0, 0.15 M LI2(SO4)
Crystal Properties
Matthews coefficientSolvent content
2.5142

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.43α = 90
b = 79.2β = 90
c = 30.78γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray123IMAGE PLATERIGAKU RAXIS IIMSC-YALE MIRRORS1997-04-04M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH2R

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
11.6635.26720.0420.051142.5167202
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)
1.61.86370.0870.133.62.5

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 1PKR1.66711672015014840.16615.4
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]
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor22.4
p_staggered_tor17.8
p_planar_tor5.2
p_multtor_nbd0.24
p_xyhbond_nbd0.23
p_singtor_nbd0.18
p_chiral_restr0.16
p_planar_d0.05
p_angle_d0.034
p_bond_d0.016
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor22.4
p_staggered_tor17.8
p_planar_tor5.2
p_multtor_nbd0.24
p_xyhbond_nbd0.23
p_singtor_nbd0.18
p_chiral_restr0.16
p_planar_d0.05
p_angle_d0.034
p_bond_d0.016
p_angle_deg
p_hb_or_metal_coord
p_mcbond_it
p_mcangle_it
p_scbond_it
p_scangle_it
p_plane_restr
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1296
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms

Software

Software
Software NamePurpose
RIGAKUdata collection
RIGAKUdata reduction
AMoREphasing
PROFFTrefinement
R-AXISdata reduction
R-AXISdata scaling