5OLR | pdb_00005olr

Rhamnogalacturonan lyase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293100 mM succinic acid, sodium phosphate glycine buffer pH 6.0 and 25 % (w/v) PEG 1500
Crystal Properties
Matthews coefficientSolvent content
1.9336.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.458α = 90
b = 123.872β = 90
c = 137.628γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97949DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.0748.494.30.99811.33.2536956
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.071.0933.10.3780.91.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT1.0748.45099392688994.320.14580.14470.150.166430.17RANDOM11.582
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]
0.11-0.310.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.516
r_sphericity_free23.039
r_dihedral_angle_4_deg11.861
r_dihedral_angle_3_deg10.866
r_sphericity_bonded7.352
r_dihedral_angle_1_deg7.217
r_rigid_bond_restr4.915
r_long_range_B_refined3.443
r_long_range_B_other3.443
r_scangle_other1.822
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.516
r_sphericity_free23.039
r_dihedral_angle_4_deg11.861
r_dihedral_angle_3_deg10.866
r_sphericity_bonded7.352
r_dihedral_angle_1_deg7.217
r_rigid_bond_restr4.915
r_long_range_B_refined3.443
r_long_range_B_other3.443
r_scangle_other1.822
r_angle_refined_deg1.538
r_scbond_it1.515
r_scbond_other1.51
r_mcangle_other1.19
r_mcangle_it1.189
r_angle_other_deg1.079
r_mcbond_it0.961
r_mcbond_other0.956
r_chiral_restr0.099
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9788
Nucleic Acid Atoms
Solvent Atoms1757
Heterogen Atoms126

Software

Software
Software NamePurpose
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
Cootmodel building