1MVQ

Cratylia mollis lectin (isoform 1) in complex with methyl-alpha-D-mannose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CNAPDB ENTRY 5CNA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Vapor diffusion, microgravity4.5295PEG 6000, sodium chloride, O1-methyl-alpha-D-mannose, acetate buffer, pH 4.5, Vapor diffusion, microgravity, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.5652.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.449α = 90
b = 77.956β = 90
c = 105.323γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277IMAGE PLATEMARRESEARCHmirrorMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX11.38LNLSD03B-MX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.779.9499.60.0683.76255532555327.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.771.8198.10.0684.93.721767

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 5CNA1.779.94242652426512881000.141730.141730.140230.16991RANDOM11.688
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]
1.22-0.24-0.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg12.298
r_dihedral_angle_1_deg6.728
r_scangle_it4.633
r_scbond_it2.858
r_mcangle_it2.022
r_angle_refined_deg1.599
r_mcbond_it1.104
r_symmetry_vdw_refined0.26
r_nbd_refined0.201
r_xyhbond_nbd_refined0.133
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg12.298
r_dihedral_angle_1_deg6.728
r_scangle_it4.633
r_scbond_it2.858
r_mcangle_it2.022
r_angle_refined_deg1.599
r_mcbond_it1.104
r_symmetry_vdw_refined0.26
r_nbd_refined0.201
r_xyhbond_nbd_refined0.133
r_chiral_restr0.123
r_symmetry_hbond_refined0.095
r_bond_refined_d0.015
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1778
Nucleic Acid Atoms
Solvent Atoms179
Heterogen Atoms15

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement