3DNF

Structure of (E)-4-Hydroxy-3-methyl-but-2-enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829110 % (w/w) PEG 8000, 0,1 M Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.8857.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.37α = 90
b = 87.76β = 95.13
c = 72.4γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2007-07-01MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.983SLSX10SA

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
11.659.987.20.04515.943.57178765
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)
11.651.753.40.3213.292.3569714

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.659.977992412091.350.194290.19260.22605RANDOM35.247
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]
0.680.70.1-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.011
r_dihedral_angle_4_deg16.739
r_dihedral_angle_3_deg14.371
r_dihedral_angle_1_deg5.409
r_scangle_it3.488
r_scbond_it2.28
r_angle_refined_deg1.455
r_mcangle_it1.329
r_mcbond_it0.883
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.011
r_dihedral_angle_4_deg16.739
r_dihedral_angle_3_deg14.371
r_dihedral_angle_1_deg5.409
r_scangle_it3.488
r_scbond_it2.28
r_angle_refined_deg1.455
r_mcangle_it1.329
r_mcbond_it0.883
r_nbtor_refined0.303
r_chiral_restr0.249
r_xyhbond_nbd_refined0.21
r_nbd_refined0.203
r_symmetry_vdw_refined0.193
r_symmetry_hbond_refined0.176
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4412
Nucleic Acid Atoms
Solvent Atoms561
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
SHARPphasing