5Z5P | pdb_00005z5p

Crystal structure of ConA-R3M


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.230020% polyethylene glycol 6000, 20 mM HEPES, 100 mM NaCl, 5 mM CaCl2, 5 mM MnCl2 pH 7.2
Crystal Properties
Matthews coefficientSolvent content
2.0640.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.742α = 90
b = 61.945β = 90
c = 115.96γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.9716SSRFBL17U1

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
11.45999.72.212.484005
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.42

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 DIFFRACTIONTHROUGHOUT1.458.7472652372190.840.194920.19260.210.241490.25RANDOM18.086
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]
-0.24-0.050.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.244
r_dihedral_angle_3_deg13.967
r_dihedral_angle_4_deg12.757
r_dihedral_angle_1_deg9.223
r_long_range_B_refined6.316
r_long_range_B_other6.315
r_scangle_other3.967
r_mcangle_it3.386
r_mcangle_other3.386
r_angle_refined_deg2.647
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.244
r_dihedral_angle_3_deg13.967
r_dihedral_angle_4_deg12.757
r_dihedral_angle_1_deg9.223
r_long_range_B_refined6.316
r_long_range_B_other6.315
r_scangle_other3.967
r_mcangle_it3.386
r_mcangle_other3.386
r_angle_refined_deg2.647
r_scbond_it2.615
r_scbond_other2.614
r_mcbond_it2.209
r_mcbond_other2.206
r_angle_other_deg1.26
r_chiral_restr0.303
r_bond_refined_d0.025
r_gen_planes_refined0.013
r_gen_planes_other0.003
r_bond_other_d0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3399
Nucleic Acid Atoms
Solvent Atoms290
Heterogen Atoms123

Software

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