4CNN | pdb_00004cnn

High resolution structure of Salmonella typhi type I dehydroquinase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QFEPDB ENTRY 1QFE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.430% PEG 4000, 0.1 M CITRATE-PHOSPHATE PH 6.4
Crystal Properties
Matthews coefficientSolvent content
2.141.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.273α = 90
b = 44.422β = 95.19
c = 84.711γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MPLANE-ELLIPSOIDAL MIRRORS (SI, RH, IR)2013-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOCALBAXALOC

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
1184.3679.30.0319.73.6190168-38.6
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)
111.0526.50.432.32.6

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1QFE151.2186322382379.040.131680.131340.140.148720.16RANDOM11.478
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]
0.520.06-0.02-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.218
r_sphericity_free26.658
r_dihedral_angle_4_deg20.175
r_dihedral_angle_3_deg13.119
r_sphericity_bonded6.155
r_scbond_it6.013
r_dihedral_angle_1_deg5.509
r_mcangle_it4.433
r_mcbond_it3.225
r_scangle_it2.463
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.218
r_sphericity_free26.658
r_dihedral_angle_4_deg20.175
r_dihedral_angle_3_deg13.119
r_sphericity_bonded6.155
r_scbond_it6.013
r_dihedral_angle_1_deg5.509
r_mcangle_it4.433
r_mcbond_it3.225
r_scangle_it2.463
r_mcbond_other1.378
r_angle_refined_deg1.264
r_rigid_bond_restr1.144
r_angle_other_deg0.778
r_symmetry_vdw_refined0.262
r_nbd_refined0.249
r_symmetry_vdw_other0.202
r_nbtor_refined0.174
r_nbd_other0.169
r_symmetry_hbond_refined0.164
r_xyhbond_nbd_refined0.132
r_nbtor_other0.084
r_chiral_restr0.077
r_xyhbond_nbd_other0.062
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3782
Nucleic Acid Atoms
Solvent Atoms752
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEdata scaling
MOLREPphasing