5CCU

Crystal structure of endoglycoceramidase I from Rhodococ-cus equi


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OSW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7294PEG 6000 MES sodium hydroxide Ammonium chloride
Crystal Properties
Matthews coefficientSolvent content
2.448.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 192.841α = 90
b = 48.98β = 114.3
c = 120.304γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.979SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.1085098.410.094.258536
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.18964.3

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 REPLACEMENTTHROUGHOUT2OSW2.115055593294397.90.1860.1840.218RANDOM22.21
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]
-0.91-0.631.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.655
r_dihedral_angle_4_deg17.545
r_dihedral_angle_3_deg13.265
r_dihedral_angle_1_deg5.727
r_long_range_B_refined3.132
r_long_range_B_other3.132
r_scangle_other1.129
r_mcangle_it1.122
r_mcangle_other1.122
r_angle_refined_deg1.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.655
r_dihedral_angle_4_deg17.545
r_dihedral_angle_3_deg13.265
r_dihedral_angle_1_deg5.727
r_long_range_B_refined3.132
r_long_range_B_other3.132
r_scangle_other1.129
r_mcangle_it1.122
r_mcangle_other1.122
r_angle_refined_deg1.073
r_angle_other_deg0.746
r_scbond_it0.638
r_scbond_other0.638
r_mcbond_it0.619
r_mcbond_other0.619
r_chiral_restr0.059
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.002
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 Atoms6803
Nucleic Acid Atoms
Solvent Atoms467
Heterogen Atoms77

Software

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