2FD7

X-ray Crystal Structure of Chemically Synthesized Crambin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298The native crambin crystals were grown from the aqueous solution by mixing a 2 ul aliquot of a crambin (10 mg/ml in pH 8.0, 100mM HEPES buffer containing 150mM NaCl) and 2 ul of a 0.8 M succinic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.924α = 90
b = 104.924β = 90
c = 104.924γ = 90
Symmetry
Space GroupI 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID1.0000APS19-ID

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
11.753095199070
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.795

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT1.7530907044992.750.160140.160140.158870.18476RANDOM22.323
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.268
r_dihedral_angle_4_deg25.067
r_dihedral_angle_3_deg11.381
r_dihedral_angle_1_deg4.982
r_scangle_it2.831
r_angle_other_deg2.256
r_scbond_it1.933
r_angle_refined_deg1.491
r_mcangle_it1.105
r_mcbond_it0.977
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.268
r_dihedral_angle_4_deg25.067
r_dihedral_angle_3_deg11.381
r_dihedral_angle_1_deg4.982
r_scangle_it2.831
r_angle_other_deg2.256
r_scbond_it1.933
r_angle_refined_deg1.491
r_mcangle_it1.105
r_mcbond_it0.977
r_nbd_refined0.221
r_mcbond_other0.205
r_nbd_other0.193
r_symmetry_hbond_refined0.175
r_xyhbond_nbd_refined0.148
r_symmetry_vdw_other0.134
r_nbtor_other0.084
r_chiral_restr0.063
r_xyhbond_nbd_other0.055
r_bond_refined_d0.014
r_symmetry_vdw_refined0.014
r_bond_other_d0.005
r_gen_planes_refined0.005
r_gen_planes_other0.001
r_nbtor_refined
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms325
Nucleic Acid Atoms
Solvent Atoms80
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement