2ZUY

Crystal structure of exotype rhamnogalacturonan lyase YesX


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Z8RPDB ENTRY 2Z8R

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.129320% PEG 3350, 0.2M Ammonium acetate, pH7.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3146.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.853α = 90
b = 88.07β = 90
c = 99.304γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 210mirror2008-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.000SPring-8BL38B1

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
11.655098.90.0948.29.877151
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)
1.651.7197.40.2584.19.1

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 2Z8R1.6537.1972362383898.730.161770.160540.18425RANDOM10.801
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.544
r_dihedral_angle_4_deg17.444
r_dihedral_angle_3_deg12.392
r_dihedral_angle_1_deg5.995
r_scangle_it1.93
r_scbond_it1.261
r_angle_refined_deg1.104
r_mcangle_it0.806
r_mcbond_it0.479
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.544
r_dihedral_angle_4_deg17.444
r_dihedral_angle_3_deg12.392
r_dihedral_angle_1_deg5.995
r_scangle_it1.93
r_scbond_it1.261
r_angle_refined_deg1.104
r_mcangle_it0.806
r_mcbond_it0.479
r_nbtor_refined0.305
r_nbd_refined0.194
r_symmetry_vdw_refined0.163
r_metal_ion_refined0.146
r_symmetry_hbond_refined0.101
r_xyhbond_nbd_refined0.088
r_chiral_restr0.075
r_bond_refined_d0.007
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4985
Nucleic Acid Atoms
Solvent Atoms706
Heterogen Atoms9

Software

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