2GRJ

Crystal structure of Dephospho-CoA kinase (EC 2.7.1.24) (Dephosphocoenzyme A kinase) (tm1387) from THERMOTOGA MARITIMA at 2.60 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP5.229330.0M NaCl, 32.5% PEG-8000, 0.1M Na,K-Phosphate pH 5.2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.142.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.832α = 90
b = 87.217β = 106.92
c = 98.586γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2003-07-13MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-B0.97921, 0.9537246, 0.97907APS14-ID-B

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
12.647.796.80.077.793.374470140.15
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)
12.62.6974.70.3751.84

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)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 DIFFRACTIONMADTHROUGHOUT2.625.2944609224998.410.1930.193280.1910.245RANDOM35.699
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]
0.661.01-1.921.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.132
r_dihedral_angle_3_deg16.457
r_dihedral_angle_4_deg15.29
r_scangle_it6.649
r_dihedral_angle_1_deg5.622
r_scbond_it4.645
r_mcangle_it2.158
r_angle_refined_deg1.791
r_mcbond_it1.742
r_angle_other_deg0.899
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.132
r_dihedral_angle_3_deg16.457
r_dihedral_angle_4_deg15.29
r_scangle_it6.649
r_dihedral_angle_1_deg5.622
r_scbond_it4.645
r_mcangle_it2.158
r_angle_refined_deg1.791
r_mcbond_it1.742
r_angle_other_deg0.899
r_mcbond_other0.251
r_nbd_refined0.229
r_symmetry_hbond_refined0.186
r_nbd_other0.177
r_nbtor_refined0.176
r_symmetry_vdw_refined0.158
r_symmetry_vdw_other0.14
r_xyhbond_nbd_refined0.133
r_nbtor_other0.088
r_chiral_restr0.085
r_bond_refined_d0.016
r_gen_planes_refined0.005
r_gen_planes_other0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10846
Nucleic Acid Atoms
Solvent Atoms67
Heterogen Atoms572

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing