8IDR

Crystal structure of apo-form of dehydroquinate dehydratase from Corynebacterium glutamicum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1V1J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293.15PEG 3350, Ammonium citrate tribasic
Crystal Properties
Matthews coefficientSolvent content
2.2846.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.531α = 90
b = 81.531β = 90
c = 221.807γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702022-05-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.97934PAL/PLS7A (6B, 6C1)

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
11.850990.06517.92.747482
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)
11.81.83990.2742.7

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.826.5147482249497.950.160060.157780.20279RANDOM24.309
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]
0.40.20.4-1.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.705
r_dihedral_angle_4_deg15.071
r_dihedral_angle_3_deg12.979
r_dihedral_angle_1_deg6.591
r_long_range_B_refined6.018
r_long_range_B_other5.885
r_scangle_other4.249
r_scbond_it2.939
r_scbond_other2.936
r_mcangle_other2.817
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.705
r_dihedral_angle_4_deg15.071
r_dihedral_angle_3_deg12.979
r_dihedral_angle_1_deg6.591
r_long_range_B_refined6.018
r_long_range_B_other5.885
r_scangle_other4.249
r_scbond_it2.939
r_scbond_other2.936
r_mcangle_other2.817
r_mcangle_it2.813
r_mcbond_it1.977
r_mcbond_other1.959
r_angle_refined_deg1.587
r_angle_other_deg1.447
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4369
Nucleic Acid Atoms
Solvent Atoms589
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing