1KJJ

Crystal structure of glycniamide ribonucleotide transformylase in complex with Mg-ATP-gamma-S


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EYZPDB ENTRY 1EYZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1batch6.7277PEG 5000, NaCl, MgCl2, MOPS, ATP-gamma-S, pH 6.7, batch at 277K
Crystal Properties
Matthews coefficientSolvent content
2.4950.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.9α = 90
b = 179.3β = 90
c = 76.1γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110AREA DETECTORSIEMENS HI-STARgoebel optics2000-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54178

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
11.7530960.0618.22.58269582695
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)
1.751.87880.2154.41.49407

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1EYZ1.753082695826958270960.1870.1870.1840.233RANDOM
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
t_angle_deg2.6
t_bond_d0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5892
Nucleic Acid Atoms
Solvent Atoms674
Heterogen Atoms81

Software

Software
Software NamePurpose
TNTrefinement
FRAMBOdata collection
SAINTdata scaling
TNTphasing