1ZNY | pdb_00001zny

Crystal Structure Of Mycobacterium tuberculosis Guanylate Kinase In Complex With GDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZNW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529315% (w/v) xylitol, 3.5M sodium chloride, 0.1M sodium Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.7455.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.046α = 90
b = 113.046β = 90
c = 113.046γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4mirrors2003-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9756ESRFID29

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
12.32099.70.08332.232.8108291082947
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.3012.361000.45810.333.3791

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1ZNW2.320108341029753799.910.186410.186410.183920.190.235810.19RANDOM24.798
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
r_dihedral_angle_1_deg5.909
r_scangle_it3.335
r_scbond_it2.023
r_angle_refined_deg1.572
r_mcangle_it1.253
r_angle_other_deg0.883
r_mcbond_it0.667
r_nbd_other0.231
r_symmetry_vdw_other0.228
r_nbd_refined0.213
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1389
Nucleic Acid Atoms
Solvent Atoms57
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
XSCALEdata scaling
CCP4phasing