4ASM

Crystal structure of the catalytic domain of beta-agarase D from Zobellia galactanivorans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O4ZPDB ENTRY 1O4Z

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1828-34 % PEG 8000 AND 0,1 M IMIDAZOLE PH 8, 4% ISOPROPANOL
Crystal Properties
Matthews coefficientSolvent content
2.1442

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.247α = 90
b = 77.268β = 90
c = 83.695γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102008-10-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.55699.90.0521.36.9559770.1
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)
11.51.5899.90.259.16.9

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 1O4Z1.556.853071283999.850.163540.162150.18987RANDOM13.7
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]
0.06-0.03-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.495
r_dihedral_angle_4_deg18.631
r_dihedral_angle_3_deg12.873
r_dihedral_angle_1_deg6.981
r_scangle_it2.82
r_scbond_it1.958
r_angle_refined_deg1.441
r_mcangle_it1.283
r_angle_other_deg0.876
r_mcbond_it0.784
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.495
r_dihedral_angle_4_deg18.631
r_dihedral_angle_3_deg12.873
r_dihedral_angle_1_deg6.981
r_scangle_it2.82
r_scbond_it1.958
r_angle_refined_deg1.441
r_mcangle_it1.283
r_angle_other_deg0.876
r_mcbond_it0.784
r_nbd_other0.324
r_nbtor_refined0.31
r_symmetry_vdw_refined0.232
r_nbd_refined0.209
r_xyhbond_nbd_refined0.2
r_symmetry_hbond_refined0.179
r_chiral_restr0.127
r_metal_ion_refined0.075
r_nbtor_other0.048
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.005
r_gen_planes_other
r_xyhbond_nbd_other
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2843
Nucleic Acid Atoms
Solvent Atoms595
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing