5E16

Co-crystal structure of the N-termial cGMP binding domain of Plasmodium falciparum PKG with cGMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4MYJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529325 % Peg3350, 0.2 M NaCl, 0.1 M HEPES, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
1.9837.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.266α = 90
b = 53.847β = 90
c = 92.351γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002015-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.655099.70.0430.0460.01719.47.415745
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.6896.80.3030.3340.1380.9575.6750

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 REPLACEMENTTHROUGHOUT4MYJ1.6546.181485181399.220.19720.19550.2268RANDOM27.091
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]
0.710.64-1.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.808
r_dihedral_angle_4_deg16.009
r_dihedral_angle_3_deg11.899
r_dihedral_angle_1_deg5.985
r_mcangle_it3.015
r_mcbond_it2.006
r_mcbond_other1.994
r_angle_refined_deg1.592
r_angle_other_deg0.951
r_chiral_restr0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.808
r_dihedral_angle_4_deg16.009
r_dihedral_angle_3_deg11.899
r_dihedral_angle_1_deg5.985
r_mcangle_it3.015
r_mcbond_it2.006
r_mcbond_other1.994
r_angle_refined_deg1.592
r_angle_other_deg0.951
r_chiral_restr0.093
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1078
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms23

Software

Software
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing