1H3M

Structure of 4-diphosphocytidyl-2C-methyl-D-erythritol synthetase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1INIPDB ENTRY 1INI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
160.2M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE, PH 5.6, 25% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.2350.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.604α = 90
b = 73.604β = 90
c = 175.562γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
12.42099.50.03374196191.5
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)
12.42.4698.60.273.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1INI2.42018554100099.70.2410.2370.333RANDOM49.08
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]
1.211.21-2.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.195
r_scangle_it3.784
r_scbond_it2.35
r_mcangle_it1.737
r_angle_refined_deg1.668
r_mcbond_it0.944
r_symmetry_vdw_refined0.28
r_symmetry_hbond_refined0.267
r_nbd_refined0.229
r_xyhbond_nbd_refined0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.195
r_scangle_it3.784
r_scbond_it2.35
r_mcangle_it1.737
r_angle_refined_deg1.668
r_mcbond_it0.944
r_symmetry_vdw_refined0.28
r_symmetry_hbond_refined0.267
r_nbd_refined0.229
r_xyhbond_nbd_refined0.17
r_chiral_restr0.107
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3307
Nucleic Acid Atoms
Solvent Atoms86
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing