3ESJ | pdb_00003esj

Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GX1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52982M ammonium formate, HEPES, 5% butanediol, pH 7.5, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
7.15227582.802673

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.498α = 90
b = 144.498β = 90
c = 144.498γ = 90
Symmetry
Space GroupI 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210mirrors2003-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9756ESRFID29

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
12.729.49599.90.0990.0995.99514.5139468.9
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)
2.72.851000.2740.2742.714.72025

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 (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1GX12.724.69137951378669099.930.1860.1840.190.2180.22RANDOM40.065
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_2_deg35.792
r_dihedral_angle_3_deg19.381
r_dihedral_angle_4_deg16.282
r_dihedral_angle_1_deg6.139
r_scangle_it2.979
r_scbond_it1.764
r_mcangle_it1.631
r_angle_refined_deg1.551
r_mcbond_it0.999
r_symmetry_vdw_refined0.341
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.792
r_dihedral_angle_3_deg19.381
r_dihedral_angle_4_deg16.282
r_dihedral_angle_1_deg6.139
r_scangle_it2.979
r_scbond_it1.764
r_mcangle_it1.631
r_angle_refined_deg1.551
r_mcbond_it0.999
r_symmetry_vdw_refined0.341
r_nbtor_refined0.319
r_nbd_refined0.237
r_symmetry_hbond_refined0.183
r_xyhbond_nbd_refined0.131
r_chiral_restr0.091
r_metal_ion_refined0.058
r_symmetry_metal_ion_refined0.015
r_bond_refined_d0.013
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1215
Nucleic Acid Atoms
Solvent Atoms97
Heterogen Atoms41

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction