2HQ1

Crystal Structure of ORF 1438 a putative Glucose/ribitol dehydrogenase from Clostridium thermocellum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EDOPDB entry 1EDO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1HANGING DROP VAPOR DIFUSION USING 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION (9 MG/ML) AND A PRECIPITANT SOLUTION CONTAINING 0.1M AMMONIUM DIHYDROGEN PHOSPHATE AND 20% W/V PEG 3350, SETUP AT 291K.
Crystal Properties
Matthews coefficientSolvent content
2.5952.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.982α = 90
b = 99.487β = 90
c = 69.833γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDRosenbaum2006-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.9790APS22-ID

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
11.92092.680.05321.26.620685191282
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)
1.91.9757.90.3523.233.81282

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMolecular ReplacemetTHROUGHOUTPDB entry 1EDO1.9201912819128104592.680.233210.233210.232350.24902RANDOM23.136
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]
-1.361.9-0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.909
r_dihedral_angle_3_deg14.363
r_dihedral_angle_4_deg11.654
r_dihedral_angle_1_deg4.926
r_scangle_it2.035
r_scbond_it1.333
r_angle_refined_deg1.054
r_mcangle_it0.935
r_mcbond_it0.542
r_nbtor_refined0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.909
r_dihedral_angle_3_deg14.363
r_dihedral_angle_4_deg11.654
r_dihedral_angle_1_deg4.926
r_scangle_it2.035
r_scbond_it1.333
r_angle_refined_deg1.054
r_mcangle_it0.935
r_mcbond_it0.542
r_nbtor_refined0.294
r_nbd_refined0.181
r_symmetry_vdw_refined0.151
r_symmetry_hbond_refined0.121
r_xyhbond_nbd_refined0.104
r_chiral_restr0.066
r_bond_refined_d0.009
r_gen_planes_refined0.003
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 Atoms1548
Nucleic Acid Atoms
Solvent Atoms54
Heterogen Atoms

Software

Software
Software NamePurpose
CCP4model building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing