3D5H

Crystal structure of haementhin from Haemanthus multiflorus at 2.0A resolution: Formation of a novel loop on a TIM barrel fold and its functional significance


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.22980.1M ammonium sulphate, 20% PEG 6000, 0.1M sodium acetate, 20mM phosphate buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2745.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.803α = 90
b = 65.4β = 102
c = 49.435γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMAR scanner 345 mm plateMirror2007-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54132

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
1248.22497.51813116787
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.0597.6

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 REPLACEMENTTHROUGHOUT2HVM248.22181311678788997.50.170.153720.151930.18632RANDOM26.53
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]
-0.23-0.15-0.040.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.247
r_dihedral_angle_1_deg4.912
r_scangle_it4.722
r_scbond_it2.992
r_mcangle_it2.05
r_angle_refined_deg1.811
r_mcbond_it1.112
r_symmetry_hbond_refined0.244
r_nbd_refined0.226
r_symmetry_vdw_refined0.199
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.247
r_dihedral_angle_1_deg4.912
r_scangle_it4.722
r_scbond_it2.992
r_mcangle_it2.05
r_angle_refined_deg1.811
r_mcbond_it1.112
r_symmetry_hbond_refined0.244
r_nbd_refined0.226
r_symmetry_vdw_refined0.199
r_xyhbond_nbd_refined0.178
r_chiral_restr0.147
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2108
Nucleic Acid Atoms
Solvent Atoms300
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing